Hosts and fermentation processes for cellulase production

ABSTRACT

A fermentation process for the production of cellulase mixtures is provided. The process comprises providing a genetically modified host filamentous fungus that overexpresses a Xyr1 transcription factor and/or that is partially or completely deficient in expressing one or more hemicellulase enzyme. The host filamentous fungus is cultured in a medium comprising a carbon source. The carbon source contains from about 60 wt % to about 100 wt % hemicellulose-derived carbohydrate and less than 5% of a cellulase-inducing carbohydrate or contains from about 25 wt % to about 100% wt % hemicellulose-derived sugar alcohol in combination with from about 0 wt % to about 75 wt % glucose, glycerol or a combination thereof.

FIELD OF THE INVENTION

The present invention relates to a fermentation process for the production of a cellulase mixture. More specifically, the present invention relates to a fermentation process comprising the use of genetically modified filamentous fungi hosts for the production of a cellulase mixture.

BACKGROUND OF THE INVENTION

Plant cell walls consist mainly of the large biopolymers cellulose, hemicellulose, lignin and pectin. Cellulose and hemicellulose constitute an important renewable and inexpensive carbon source for the production of fermentable sugars. Cellulose consists of D-glucose units linked together in linear chains via beta-1,4 glycosidic bonds. Hemicellulose consists primarily of a linear xylan backbone comprising D-xylose units linked together via beta-1,4 glycosidic bonds and numerous side chains linked to the xylose units via beta-1,2 or beta-1,3 glycosidic or ester bonds (e.g., L-arabinose, acetic acid, ferulic acid, etc).

Filamentous fungi of the phylum (division) Ascomycota, including various Penicillium, Phanerochaete, Agaricus, Neurospora, Humicola, Fusarium, Chaetomium, Magnaporthe, Aspergillus and Trichoderma species, have a key role in degradation of the most abundant polymers found in nature, cellulose and hemicellulose. Trichoderma reesei (the asexual anamorph of Hypocrea jecorina) is an important industrial source of cellulase and hemicellulase enzymes. The term cellulase (or cellulase enzymes) broadly refers to enzymes that catalyze the hydrolysis of the beta-1,4-glucosidic bonds joining individual glucose units in the cellulose polymer. The catalytic mechanism involves the synergistic actions of endoglucanases (E.C. 3.2.1.4), cellobiohydrolases (E.C. 3.2.1.91) and beta-glucosidase (E.C. 3.2.1.21). The term hemicellulase broadly refers to enzymes that catalyze the hydrolysis of the various glycosidic bonds joining individual xylose, arabinose, mannose, galactose and other moieties in the hemicellulose polymer. Hemicellulases include, for example, endo-1,4-beta-xylanases (EC 3.2.1.8), beta-mannanases (EC 3.2.1.28), alpha-L-arabinofuranosidases (EC 3.2.1.55), 1,4-beta-xylosidase (EC 3.2.1.27) and alpha-glucuronidase (EC 3.2.1.139).

Trichoderma reesei is a commonly used industrial species of filamentous fungi for the production of biomass degrading enzymes such as cellulases and hemicellulases. Analysis of the secretome of T. reesei strain RutC30 revealed the presence of 31 secreted glycosyl hydrolases when grown in media supplemented with pretreated corn stover (Nagendran et al., 2009) Studies of the secretome of F. graminearum grown on hop cell wall identified that at least 45% of the secreted proteins are involved in plant cell wall degradation, with 25, 19 and 11 different proteins for hemicellulose, pectin and cellulose degradation, respectively (Phalip et al., 2005).

Sequencing and analysis of the T. reesei genome has revealed the presence of 10 genes encoding cellulase and 16 genes encoding hemicellulases (Martinez et al., 2008). These include two cellobiohydrolases, eight endoglucanases, four xylanases, two alpha-L-arabinofuranosidases, and a beta-mannanase. T. reesei also produces a number of accessory enzymes that assist in the generation of monosaccharides from the cellulose and hemicellulose, including acetyl xylan esterase, beta-xylosidase and several beta-glucosidases (de Vries and Visser, 2001; Aro et al., 2005, and references therein). However, when compared with the genomes of other filamentous fungi, the T. reesei genome has surprisingly few genes encoding glycoside hydrolases (total 200) (Martinez et al., 2008). For example, Aspergillus oryzae, Aspergillus fumigatus, Aspergillus nidulans and Fusarium graminearum encodes 285, 263, 247 and 243 glycosyl hydrolases, respectively (Martinez et al., 2008).

The production of plant cell wall degrading enzymes such as cellulases, hemicellulases, ligninases and pectinases, by filamentous fungi is regulated mainly at the transcriptional level in response to available carbon sources. Glucose represses cellulase gene expression through the action of transcriptional regulators such as cre1 (Strauss et al., 1995,). Under glucose-limiting conditions, cellulase transcription is derepressed, with full activation of transcription requiring the presence of a cellulase-inducing carbohydrate, or inducer, such as cellulose, or beta-linked disaccharides such as cellobiose, sophorose, gentiobiose and lactose (Ilmen et al., 1997), while activation of hemicellulase transcription is dependent on the presence of xylan or its derivatives (xylose, xylobiose, arabinose) in the growth media (Margolles-Clark et al., 1997).

The transcriptional regulator XlnR (xylanase regulator), initially identified in Aspergillus niger, controls the transcription of about 20-30 genes encoding hemicellulases and cellulases (Stricker et al, 2008 and references therein). Moreover, the extracellular xylan degradation and intracellular D-xylose metabolism is coupled via the transcriptional regulation of the xyrA (D-xylose reductase-encoding) gene by XlnR (Hasper et al, 2000). The orthologous transcription factors in T. reesei, Xyr1 (xylanase regulator 1) and Aspergillus oryzae (Ao XlnR) are also a general regulators of cellulase and hemicellulase gene expression (Striker et al, 2006; Marui et al, 2002). Studies of several other identified regulators of xylanase expression in fungi are limited to the regulation of hemicellulase genes (Tamayo et al, 2008; Rao et al, 2002; Calero-Nieto et al, 2007). For examples, it has been shown that deletion of an orthologous transcription factor to Xyr1 from Fusarium graminearum did not affect the basic expression levels of xylanases and cellulases but did prevent high inducible expression (Brunner et al, 2007). This finding is in contradiction to the studies with Trichoderma and Aspergillus, where the knock out of the corresponding regulator abolishes cellulase and xylanase expression completely. These observations led to a system for production of homologous and/or hetereologous proteins using XlnR regulated promoter along with overexpression of xylanase regulator, XlnR, from multiple gene copies (U.S. Pat. No. 6,177,261 B1, 2001).

Xylanase regulators, such as Xyr1 from Trichoderma and XlnR from Aspergillus, belong to class III zinc binuclear cluster protein family found exclusively in fungi and possess a conserved amino acid motif (CX₂CX₆CX₅₋₁₂CX₂CX₆₋₈C) at the N-terminal part of the protein (MacPherson et al., 2006). This class of transcription factors is unique in containing only one zinc finger that binds two zinc atoms. Xylanase regulators bind 5′-GGC(T/A)₃-3′ response elements in the promoters of target genes, and may interact with DNA as monomers, homodimers or heterodimers (MacPherson et al., 2006; Stricker et al., 2008). Several studies have shown that T. reesei Xyr1 is essential for the expression of all major (hemi)cellulase genes (Stricker et al., 2006) and that it binds to xylanase 1, 2 and 3 gene promoters (Rauscher et al, 2006; Stricker et al, 2007; Furukawa et al, 2009). However, in vitro binding of T. reesei Xyr1 to cellulase gene promoters was only recently demonstrated (Furukawa et al, 2009; Ling et al., 2009). In silico analysis has revealed that the 5′-GGC(T/A)₃-3′ motifs are widespread as single sites in 5′-upstream region of all Xyr1-regulated genes in T. reesei (Furukawa et al, 2009). However in vitro studies of Xyr1 binding to selected motifs revealed that only several of them can be recognized by this transcription factor (Furukawa et al, 2009).

Other functional domains have been identified for A. niger XlnR by loss-of-function mutations and rational design mutagenesis analyses (Hasper et al., 2004). These studies demonstrated that the second putative coiled-coil domain is involved in the nuclear localization of the protein. Protein structure predictions suggest the presence of two coiled-coil domains at similar positions in A. niger XlnR and T. reesei Xyr1. Thus, the second coiled-coil domain of T. reesei Xyr1 may likewise be responsible for its transport into the nucleus. The C-terminus of XlnR is essential for transcriptional regulation; deletion of 78 C-terminal amino acids causes increased expression of XlnR target genes, even under glucose repression conditions, suggesting this region dampens transcriptional activation by XlnR (Hasper et al., 2004). However, certain single-amino acid mutations in this region such as Tyr864Phe, Leu823Ser and Tyr864Asp lead to severely diminished activation by XlnR (Hasper et al., 2004).

Although A. niger XlnR and T. reesei Xyr1 share similarities in structure and in consensus binding sites, there is evidence to suggest that these factors interact with promoters via different mechanisms. For example, it was suggested that A. niger XlnR binds as a monomer (Hasper et al., 2004), while T. reesei Xyr1 binds to an inverted repeat within a regulated gene promoter, as either a homo- or a heterodimer with Ace2, a known positive regulator of cellulase expression in T. reesei (Stricker et al., 2006, 2008). It is also hypothesized that regulation of hemicellulase and cellulase gene expression in T. reesei by Xyr1 and Ace2 may involve phosphorylation and recruitment of other regulatory proteins (Stricker et al., 2008). T. reesei Xyr1 also has an antagonistic relationship with Ace1, a negative regulator of cellulase genes, through a possible competition of the two factors for the same binding site within cellulase promoters (Stricker et al, 2006). Putative Ace1-encoding genes were isolated from several other fungal species, such as Aspergillus nidulans, Talaromyces emersonii, and Neurospora crassa (Aro et al, 2005); however, their possible interaction with XlnR and their participation in transcriptional activation of hydrolase-encoding genes has not yet been shown (Stricker et al., 2006).

T. reesei produces low levels of xylanase activity under cellulase-inducing conditions; however, the enzyme system produced by cultures of T. reesei growing on xylan, xylose and arabinose, is enriched in hemicellulase activities relative to cellulase activities (Mach and Zeilinger 2003; Margolles-Clark et al., 1997; Xiong et al., 2004). This could be beneficial when the goal is to produce an enzyme composition having high xylanolytic activity relative to cellulase activity, as in the animal feed and pulp and paper industry. U.S. Pat. Nos. 6,300,112 and 5,298,405 disclose the use of cellulase-deletion strains as an alternative approach to the production of hemicellulase-enriched enzyme preparations for use in animal feed and for bio-bleaching applications

There are situations in which it is desirable to produce cellulase mixtures with a high cellulase specific activity from fungal cultures using carbohydrate sources comprising mainly xylose and other pentose sugars derived from hemicellulose, such as those produced by chemical treatments of lignocellulosic biomass. These may contain HDC or CIC However, such carbon sources result in enzyme compositions containing high hemicellulase activity with decreased cellulase specific activity, and, as a consequence, higher dosages of total protein are needed for effective hydrolysis of cellulose. Further, the production and secretion of hemicellulase enzymes uses cell energetic and secretion pathway resources and limits the cellulase expression and secretion capacity of the host cell.

It has been reported that a combination of xylan-derived carbohydrates with cellulase inducers such as cellobiose or lactose can lead to different proportions of cellulase and hemicellulase in the protein mixture secreted by Trichoderma reesei (Zeilinger, S., et al., 1996,). In addition, it has been found that concentrations of inducer (need to define) of 8 (check)-15% can improve protein production on hemicellulose derived carbohydrate (HDC) almost up to the levels produced when cellulase inducing carbohydrates are used as the carbon source. (See co-pending U.S. application Ser. No. 12/200,492). However, due to high cost of inducing carbohydrates, the use of such mixtures on a large scale can significantly increase enzyme production costs. Moreover, a significant proportion of such an enzyme mix will still be composed of hemicellulases. Consequently, due to the high content of hemicellulases, and the requirement of adding cellulase inducing carbohydrates, the production of cellulase on hemicellulase derived carbohydrates is currently not cost effective.

Thus, there is a need in the art for a cost-effective method of producing a cellulase mixtures containing low levels of hemicellulase activity from filamentous fungi using primarily hemicellulose derived carbohydrate (HDC) in the absence of the cellulase inducing carbohydrates, such as cellulose, or β-linked disaccharides such as cellobiose, sophorose, gentiobiose and lactose, or containing low levels of such carbohydrates.

SUMMARY OF THE INVENTION

The present invention relates to a fermentation process for the production of cellulase mixtures with a high proportion of cellulase components using genetically modified filamentous fungi provided with a carbon source comprising hemicellulose-derived carbohydrates (HDC) in the absence of, or containing low levels of, traditional cellulase inducing carbohydrates (CIC). The process and genetic modifications described herein can be used for the development of fungal strains producing high yields of high quality cellulase enzymes where cellulase expression is not dependent on the presence or absence of cellulase inducible carbohydrates.

The host filamentous fungus is genetically modified to overexpress a Xyr1 transcription factor or a Xyr1 equivalent transcription factor. This genetic modification results in the production of a cellulase mixture enriched in cellulase activity when the host filamentous fungus is supplied with a carbon source containing hemicellulose-derived carbohydrate and low levels of a cellulase inducing carbohydrate.

The present invention provides a fermentation process for the production of a cellulase mixture comprising: a) providing a genetically modified host filamentous fungus that overexpresses a Xyr1 transcription factor or a Xyr1 equivalent transcription factor and b) culturing the host filamentous fungus of step a) in a medium comprising a carbon source containing from about 60 wt % to about 100 wt % hemicellulose-derived carbohydrate and from about 0 wt % to about 3 wt % of a cellulase-inducing carbohydrate or in a medium comprising a carbon source containing from about 25 wt % to about 100 wt % of a hemicellulose-derived sugar alcohol, about 0% cellulase-inducing carbohydrate and from about 0 wt % to 75 wt % glucose, glycerol or a combination thereof to produce the cellulase mixture. The cellulase mixture thus produced comprises form about 40% to about 100% cellulase components and has at least a 1.7-fold increase in cellulase activity relative to a cellulase mixture produced by a parental filamentous fungus that does not overexpress a Xyr1 transcription factor when cultured in the same medium.

The Xyr1 transcription factor that is overexpressed in the host filamentous fungus used in the fermentation process of the present invention is a protein comprising the amino acid sequence of SEQ ID NO: 27, a protein with an amino acid sequence exhibiting from about 90% to about 100% identity to the amino acid sequence of SEQ ID NO: 27. The Xyr1 equivalent transcription factor, a protein with an amino acid sequence exhibiting from about 45% to about 99% identity to the amino acid sequence of SEQ ID NO: 27, a protein with an amino acid sequence exhibitin from about 90% to about 99% identity to the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35 or a protein containing a zinc binuclear cluster that that possesses equivalent DNA binding activity specific to a consensus sequence GGC(T/A)₃-like motif within cellulase and/or hemicellulase promoter sequences as the protein with the amino acid sequence of SEQ ID NO: 27.

The host filamentous fungus used in the fermentation process of the present invention may be a species of cellulolytic fungus belonging to the subphylum Pezizomycotina. For example, the host filamentous fungus may be a species of Trichoderma, Hypocrea, Aspergillus, Fusarium, Penicillium, or Neurospora. Preferably, the host filamentous fungus is Trichoderma reesei or Hypocrea jecorina.

In a first embodiment of the fermentation process of the present invention, the host filamentous comprises a Xyr1 genetic construct in which a nucleic acid sequence encoding a Xyr1 transcription factor or a Xyr1 equivlalent transcription factor is operatively linked to a promoter nucleic acid sequence. The host filamentous fungus may be produced by transformation with the Xyr1 genetic construct and selecting transformants containing the genetic construct.

The promoter nucleic acid sequence may be native or heterologous with respect to the nucleic acid sequence encoding the Xyr1 transcription factor. The promoter nucleic acid sequence may be derived from a gene whose expression is induced during growth of the host filamentous fungus on a carbon source comprising hemicellulose derived carbohydrate. For example, if the host filamentous fungus is T. reesei, the promoter nucleic acid sequence may be derived from one or more T. reesei genes encoding beta-xylosidase 1, beta-xylosidase 2, xylanase 1, xylanase 2, xylanase 3, or any combination thereof. The promoter nucleic acid sequence may also be a combination of nucleic acid sequences derived from two or more promoters. Alternately, the promoter nucleic acid sequence may be derived from a gene whose expression is constitutive during growth of the host filamentous fungus and whose expression levels are independent of the carbon source used for the fermentation process.

In a second embodiment of the fermentation process of the present invention, the modified host filamentous fungus is modified further to be partially or completely deficient in the expression of one or more hemicellulase enzymes including, but not limited to, xylanases, beta-xylosidases, alpha-arabinofuranosidases, beta-mannases, alpha-glucuronidases, acetyl xylan esterases or any combination thereof. For example, the modified host filamentous fungus may be deficient in the expression of one or more xylanases, one or more beta-xylosidases, one or more alpha-arabinofuranosidases, or any combination thereof. If the modified host filamentous fungus is a strain of T. reesei or H. jecorina, the host may be modified to be partially or completely deficient in xylanase 1, xylanase 2, beta-xylosidase 1, beta-xylosidase 2, alpha-arabinofuranosidase 1, alpha-arabinofuranosidase 2, or any combination thereof.

The carbon source provided to the host filamentous fungus during the fermentation process of the present invention may comprise other carbon sources in addition to the hemicellulose-derived carbohydrate. For example, the carbon source may comprise glycerol or other sugar alcohols such as xylitol or arabitol or an organic acid such as acetic acid or glucuronic acid.

The fermentation process of the present invention may exhibit at least about a 2-fold increase in specific productivity (q_(p)) when compared to the q_(p) of a process in which the host filamentous fungus does not overexpress Xyr1

The fermentation process of the present invention may be conducted at a temperature of from about 20° C. to about 35° C. and at a pH from about 3.0 to about 6.5 and may be carried out as a batch, fed-batch, or continuous process. Any of these modes may be operated aerobically, in the presence of oxygen, or anaerobically, in the absence of oxygen.

The present invention is based in part on the observation that cellulase mixtures with a high proportion of cellulase components can be produced by a host filamentous fungus that overexpreses a Xyr1 transcription factor in a fermentation process in which the carbon source comprises hemicellulose-derived carbohydrates (HDC) or hemicellulose-derived sugar alcohols (HDSA) in the absence, or containing low levels, of cellulase-inducing carbohydrates. The productivity of the fermentation process is significantly higher than the same process using a host filamentous fungus that does not overexpress a Xyr1 transcription factor and/or posseses wild type production levels of hemicellulases.

The fermentation process of the present invention produces a cellulase mixture that has at least about a 1.7-fold increase in cellulase activity relative to the cellulase activity of a cellulase mixture produced by a parental filamentous fungus that does not overexpress Xyr1. Cellulase components comprise about 40 wt % to about 100 wt % of the total protein present in the cellulase mixture produced by the fermentation process of the present invention. The cellulase mixture thus produced may be used in the hydrolysis of a cellulose substrate to produce glucose. For example, the cellulase mixture may be used to hydrolyze cellulose contained in a pretreated lignocellulosic feedstock.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. A—Trichoderma reesei transformation vector used for endoglucanase 2 (cel5a) deletion and generation of P285-6 strain. B—Southern hybridization using cel5a coding sequence as a probe to confirm deletion of cel5a in P285-6 and P285-4 transformants. The top panel shows the scheme of native cel5a locus and disrupted cel5a gene after targeted integration of transformation vector. The restriction sites of the enzyme used to digest genomic DNA are indicated on the bottom. The position of the probe used for Southern hybridization is indicated on the top. The lower panel shows the Southern hybridization and the name of the strain or the plasmid is indicated on the top and sizes of fragments are indicated on the left.

FIG. 2. A—Trichoderma reesei transformation vector used for xylanase 2 deletion and generation of P491P strain. B—Production of xylanase 2 in parental and transformant strains grown in microcultures on xylose as a carbon source. Aliquots (10 μg) of total secreted protein produced by parental strains (M2C38 and M2C38aux5) and transformants (P43W, P491N, P491P, P509A-G) were separated on SDS-PAGE, transferred to PVDF membrane and immunoblotted with antibodies raised against T. reesei xylanase 2. Purified Xyn2 (lane 1) was used as a control. The protein band corresponding to Xyn 2 is indicated with arrow. The weight of protein molecular weight markers is indicated in kD on the left.

FIG. 3. Relative transcript levels of cel7a (stripped bars), xyr1 (black bars) and ace1 (grey bars) genes. The biomass samples for total RNA isolation were collected at 42 h of T. reesei strain P59G fermentation time when grown on 100% arabinose, 98% xylose+2% cellobiose, or 65% glucose+35% cellulase-inducing cocktail (CIC) as the carbon source. The relative transcript levels were assessed by real time qRT-PCR and normalized to the transcription levels of the Ntf2 gene.

FIG. 4. A—Transformations vectors used to generate T. reesei transformants overexpressing xyr1. B—PCR amplification of chimeric xyr1 gene fragment from genomic DNA isolated from modified host filamentous fungal strains containing Pbxl:xyr1 expression cassettes and their parental filamentous fungal strains. Maps of the Xyr1 expression cassette are shown on the bottom of each panel. The primers used for PCR amplification are indicated by arrows. The DNA ladder was loaded in lane 1 and the size of each marker is indicated on the left. PCR products were amplified from the following templates: genomic DNA isolated from parental P285-6aux (lane 2) and modified host filamentous fungal strains P692A (lane 3), P692B (lane 4), 693A (lane 5), 693B (lane 6), water as a negative control (lane 7) and pPbxl:xyr1-pyr4 vector as a positive control (lane 8).

FIG. 5. A—The relative expression levels of xyr1, cel7a, cel7b, xyn1, xyn2, bxl1 genes in parental filamentous fungi (T. reesei P285-6) and modified host filamentous fungus overexpressing xyr1 (T. reesei strain P692) (. B—The relative expression levels of xyr1 and cel7a in parental filamentous fungi (T. reesei strain RutC30) and modified host filamentous fungi overexpressing xyr1 (T. reesei strain RutC30-R3) after 48 and 72 hrs from induction of cellulase expression. The biomass samples for total RNA isolation were prepared as described in Example 4.2. The relative transcription levels were assessed by real time qRT-PCR and normalized to the transcription levels of the Ntf2 gene. Fermentation run numbers are indicated on top of the bars.

FIG. 6. The protein (solid lines) and biomass (dotted lines) accumulation, expressed in g/L, in fermentations of modified host filamentous fungal overexpressing Xyr1 (T. reesei P692B) (A) and parental filamentous fungi (T. reesei strain P285-6) (B) strains grown on 100% xylose as a carbon source at pH 3.5.

FIG. 7. The protein (solid lines) and biomass (dotted lines) accumulation, expressed in g/L, in fermentations of modified host filamentous fungal overexpressing Xyr1 (T. reesei RutC30-R3) (A) and parental filamentous fungi (T. reesei strain RutC30) (B) strains grown on 100% xylose as a carbon source atpH 3.5.

FIG. 8. The protein (solid lines) and biomass (dotted lines) accumulation, expressed in g/L, in fermentations of T. reesei P1194E(A), P1197B (B), P491P(C) and M2C38 (D) strains grown on 100% xylose as a carbon source at pH 3.5.

FIG. 9 (A) shows the relative cellulose hydrolysis activity of the cellulase mixtures secreted by parental filamentous fungal strain P285-6 and modified host filamentous fungal strains P692B (xyr1+) and P692A (xyr1+). Cellulase mixtures are grouped based on the carbon source used for the fermentation of each of these strains. Reference numbers for the fermentations are shown along the top of the graph. (B) shows the relative abundance (in wt % of total secreted protein) of individual cellulase and xylanase components Cel7A, Cel6A, Cel7B, Xyn1 and Xyn2 in the cellulase mixtures produced by parental (strain P285-6) and modified host (strains P692B and P692A) filamentous fungi grown on 100% xylose, 100% arabinose, 25% xylose/50% glucose/25% glycerol or 25% xylitol/50% glucose/25% glycerol.

FIG. 10. (A) shows the relative cellulose hydrolysis activity of the cellulase mixtures secreted by parental filamentous fungal strain RutC30 and modified host filamentous fungal strains RutC30-R3 (xyr1+). Cellulase mixtures are grouped based on the carbon source used for the fermentation of each of these strains. Reference numbers for the fermentations are shown along the top of the graph. (B) shows the relative abundance (in wt % of total secreted protein) of individual cellulase and xylanase components Cel7A, Cel6A, Cel7B, Cel5A, Xyn1 and Xyn2 in the cellulase mixtures produced by parental (RutC30) and modified host (RutC30-R3) filamentous fungi grown on 100% xylose or 25% xylitol/50% glucose/25% glycerol.

FIG. 11. shows the relative cellulose hydrolysis activity of the cellulase mixtures secreted by parental filamentous fungi strain RutC30, M2C38 and P491P and modified host filamentous fungi stains RutC30-R3, P1194E, P1194F and P1197B (xyr1) when grown on a carbon source comprising 100% xylose or 35% CIC+65% glucose. Reference numbers for the fermentations are shown along the top of the graph.

FIG. 12. (A) shows the correlation between the relative cellulose hydrolysis activity vs. the relative proportion of cellulase components (Cel7A+Cel6A+Cel7B) of the cellulase mixtures produced by P285-6, P692B (xyr1+) and P692A (xyr1+) in fermentations using 100% xylose, 100% arabinose, 25 wt % xylose/50 wt % glucose/25% glycerol or 25% xylitol/50% glucose/25% glycerol as the carbon source. The dotted line is a linear regression analysis of all relative activity vs. cellulase component percentage for P285-6, P692B, and P692A cellulase mixtures. The r-square value derived from the linear regression was 0.75. (B) shows the correlation between the relative cellulose hydrolysis activity and vs. the relative proportion of cellulase components (Cel7A+Cel6A+Cel7B+Cel5A) in cellulase mixtures produced from RutC30 and RutC30-R3 (xyr1+). The dotted line is a linear regression analysis of all relative activity vs. cellulase components percentage for RutC30 and RutC30-R3 cellulase mixtures.

FIG. 13. Alignment of the amino acid sequence of T. reesei Xyr1 of SEQ ID NO:27 with the Xyr1 equivalent transcription factors from Aspergillus niger (identity 46.65%, SEQ ID 25), Aspergillus nidulans (identity 46.24%, SEQ ID 28), Aspergillus kawachii (identity 47.06%, SEQ ID 29), Aspergillus oryzae (identity 46.55%, SEQ ID 30), Aspergillus terreus (identity 42.83%, SEQ ID 31), Fusarium oxysporum (identity, 59.30%, SEQ ID 32), Neurospora crassa (identity 58.65%, SEQ ID 33), Penicillum canescens (identity 50.91%, SEQ ID 34), and Pyrenophora tritici-repentis (identity 42.11%, SEQ ID 35). Amino acids identical between the two sequences are shown in white font shaded in black; amino acids that are similar between the two sequences are shown in black font shaded in gray. Percent identity with T. reesei Xyr1 and the SEQ ID NO: for each sequence is indicated in brackets. The identity was calculated using DNAman program with gap penalty 3 and K-tuple 2.

FIG. 14 shows the % amino acid sequence identity for the region corresponding to amino acids 343-940 of Trichoderma reesei Xyr1 with the corresponding region between pairs of Xyr1 equivalent transcription factors from Aspergillus niger, Aspergillus oryzae Aspergillus nidulans Aspergillus terreus, Aspergillus kawachii, Neurospora crassa Penicillum canescens, Fusarium oxysporum, Pyrenophora tritici-repentis and Trichoderma reesei. 343-940 amino acids of xyr1 from T. reesei. The identity was calculated using DNAman program with gap penalty 3 and K-tuple 2.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to a fermentation process for producing cellulases from a modified host filamentous fungus.

The following description is of a preferred embodiment by way of example only and without limitation to the combination of features necessary for carrying the invention into effect.

Modified Host Filamentous Fungi

Add a sentence or two about the domain structure and where the various domains start and stop

The host filamentous fungus used in the fermentation process of the present invention is modified for increased expression of a Xyr1 transcription factor or a Xyr1 equivalent transcription factor. As used herein, a “Xyr1 transcription factor” is a protein belonging to zinc binuclear cluster family of fungal transcription factors and having an amino acid sequence from about 90% to about 100% identity to SEQ ID NO: 27 or demonstrating equivalent DNA binding activity as the T. reesei Xyr1. For example, the protein may have 90, 92, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 27, or any value therebetween.

As used herein, a Xyr1 equivalent transcription factor is a protein belonging to zinc binuclear cluster family of fungal transcription factors and having an amino acid sequence exhibiting from about 45% to about 99% identity to the amino acid sequence of SEQ ID NO: 27, a protein with an amino acid sequence exhibiting from about 90% to about 99% identity to the amino acid sequence of any one of SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35 or a protein containing a zinc binuclear cluster that that possesses equivalent DNA binding activity specific to a consensus sequence GGC(T/A)₃-like motif within cellulase and/or hemicellulase promoter sequences as the protein with the amino acid sequence of SEQ ID NO: 27.

FIG. 13 shows an alignment of the T. reesei Xyr1 transcription factor of SEQ ID NO: 27 with Xyr1 equivalent transcription factors from other fungal species. All of these enzymes exhibit from about 42% to about 59% amino acid sequence identity to SEQ ID NO: 27 (Table 1). Further, as shown in FIG. 14, amino acids corresponding to amino acids 343-940 of Trichoderma reesei Xyr1 in Xyr1 equivalent transcription factors from other cellulolytic filamentous fungi of the Subphylum Pezizomycotina exhibit from about 48% to about 66% identity to amino acids 343-940 of T. reesei Xyr1 (SEQ ID NO: 27).

TABLE 1 Xyr1 equivalent transcription factors Sequence Identity to T. reesei Xyr1 Source organism Identifier (SEQ ID NO: 27) Aspergillus niger SEQ ID NO: 25 46.65% Aspergillus nidulans SEQ ID NO: 28 46.24% Aspergillus kawachii SEQ ID NO: 29 47.06% Aspergillus oryzae SEQ ID NO: 30 46.55% Aspergillus terreus SEQ ID NO: 31 42.83% Fusarium oxysporum SEQ ID NO: 32 59.30% Neurospora crassa SEQ ID NO: 33 58.65% Penicillum canescens SEQ ID NO: 34 50.91% Pyrenophora tritici-repentis SEQ ID NO: 35 42.11%

Methods to align amino acid sequences and determine sequence identity between amino acid sequences are well known and available to those of skill in the art and include BLAST (Basic Local Alignment Search Tool, see URL blast.ncbi.nlm.nihh.gov/Blast.cgi; Altschul et al., J. Mol. Biol. 215:403-410, 1990) which is useful for aligning two sequences and CLUSTALW (see URL: ebi.ac.uk/Tools/clustalw2/index.html) for alignment of two or more sequences. Sequence identity may also be determined by manual alignment and visual inspection.

By “equivalent DNA binding activity” it is meant the DNA binding of the Xyr1 or Xyr1 equivalent transcription factor to the GGC(T/A)₃-like consensus motif mediated by a Zn₂Cys₆ zinc binuclear cluster or zinc finger domain. This cluster is well-conserved in all members of fungal zinc binuclear cluster protein family and consists of the amino acid motif Cys Xaa(2) Cys Xaa(6) Cys Xaa(5-12) Cys Xaa(2), Cys Xaa(6-8), Cys. In addition, the DNA consensus sequence recognized by the zinc binuclear cluster in the Xyr1 or Xyr1 equivalent transcription factor may be present as a single, double or triple repeat within regulated gene promoter(s). The Xyr1 or Xyr1 equivalent transcription factor may bind to the described gene promoter sequences either as a monomer or as a protein complex in either homo- or heterodimeric forms. without wishing to be bound by theory, the Xyr1 or Xyr1 equivalent transcription factor may interact with other gene-specific and/or general transcriptional factors such as Ace1 and Ace2 proteins during DNA binding. DNA binding activity of a Xyr1 or Xyr1 equivalent transcription factor to a GGC(T/A)₃-like consensus motif may be measured using one or more methods known to one of skill in the art including electrophoretic mobility-shift assay (EMSA) or DNA footprinting. Such methods are described in Furukawa, et al. 2009.

For the purpose described herein, “increased expression” or “overexpression” means at least about a 50% increase in the level of transcript for a given gene in the modified host filamentous fungus as compared to the level of transcript for the same gene in the parental filamentous fungus when grown under identical conditions of medium composition, temperature, pH, cell density and age of culture.

For the purposes described herein, by the term “parental filamentous fungus”, when used in the context of determining the expression level of the Xyr1 gene, it is meant a filamentous fungus that has not been genetically modified so as to increase expression of a Xyr1 or Xyr1 equivalent transcription factor, but which is otherwise identical to the modified host filamentous fungus.

Increased expression or overexpression of the Xyr1 or Xyr1 equivalent transcription factor may be achieved by methods known to those of skill in the art, including classical mutation and selection or genetic engineering. For example, a host cell may be genetically engineered for increased expressed of a Xyr1 or Xyr1 equivalent transcription factor by transformation of the host cell with a Xyr1 genetic construct.

As used herein, “genetic construct” refers to an isolated nucleic acid sequence comprising the nucleic acid elements necessary for the expression of a protein and the selection of host cells containing the genetic construct. These elements include, but are not limited to, a coding region comprising a nucleic acid sequence that encodes a protein product, and a promoter, comprising a nucleic acid sequence that directs the transcription of a coding region. As understood by one of ordinary skill in the art, these nucleic acid elements may be derived from the host cell or from a different organism, and/or be synthesized in vitro. These nucleic acid sequence elements may also be altered or engineered by replacement, substitution, addition, or elimination of one or more nucleic acids. The practice of this invention is not constrained by the source of or any such alterations to the nucleic acid elements comprising the genetic construct

A “Xyr1 genetic construct” refers to an isolated nucleic acid sequence comprising a coding region for a Xyr1 or Xyr1 equivalent transcription factor operably linked to a promoter. For example, the promoter may be derived from a gene that is highly expressed when the host cell is grown with a carbon source comprising HDC. For example, if the host filamentous fungus is T. reesei, the promoter nucleic acid sequence may be derived from one or more T. reesei genes encoding beta-xylosidase (JGI Protein ID 3264), beta-xylosidase 2 (JGI Protein ID 105276), xylanase 1 (JGI Protein ID 74223), xylanase 2 (JGI Protein ID 23246) o rxylanase 3 (JGI Protein ID 2034), or any combination thereof, which are available at URL: genome.jgi-psf.org/cgi-bin/browserLoad?db-Trire2). Alternatively, the promoter may be derived from a gene that is constitutively expressed. An example of a constitutive promoter in T. reesei is that derived from the phosphoglycerate kinase (pgk) gene. However, it should be understood that the practice of the present invention is not limited by the choice of promoter in the Xyr1 genetic construct.

As used herein with respect to nucleic acid sequence, “isolated” means altered from its natural state by virtue of separating the nucleic acid sequence from some or all of the naturally-occurring nucleic acid sequences with which it is associated in nature.

As used herein, in respect of nucleic acid sequence elements, “derived from” refers to the isolation of a target nucleic acid sequence element using one or more molecular biology techniques known to those of skill in the art including, but not limited to, cloning, sub-cloning, amplification by PCR, in vitro synthesis, and the like. The term “derived from” applies to both modified and native (or wild-type) nucleic acid sequence elements. In the case of native nucleic acid sequence elements, “derived from” refers to the isolation of a target nucleic acid sequence element without the introduction of one or more insertions, deletions, or substitutions to the target nucleic acid sequence elements as it is found in nature other than those that may be necessary to add to the 5′ and 3′ ends of the isolated element to facilitate cloning. In the case of modified nucleic acid sequence elements, “derived from” would also include the introduction of one or more insertions, deletions or substitutions to the wild-type or native sequence.

A genetic construct may contain a selectable marker for determining transformation of a host cell. The selectable marker may be present on the Xyr1 or other genetic construct or the selectable marker may be a separate isolated nucleic acid that is co-transformed with the genetic construct. Choices of selectable markers are well known to those skilled in the art and include genes (synthetic or natural) that confer to the transformed cells the ability to utilize a metabolite that is not normally metabolized by the microbe (e.g., the A. nidulans amdS gene encoding acetamidase and conferring the ability to grow on acetamide as the sole nitrogen source) or antibiotic resistance (e.g., the Escherichia coli hph gene encoding hygromycin-beta-phosphotransferanse and conferring resistance to hygromycin). If the host strain lacks a functional gene for the marker chosen, then that gene may be used as a marker. Examples of such markers include trp, pyr4, pyrG, argB, leu, and the like. The corresponding host strain would therefore have to be lacking a functional gene corresponding to the marker chosen, i.e., lacking in the expression of trp, pyr, arg, leu and the like.

A genetic construct may contain a transcriptional terminator that is functional in the host cell, as would be known to one of skill in the art. The transcriptional terminator may be positioned immediately downstream of a coding region. The practice of the invention is not constrained by the choice of transcriptional terminator that is sufficient to direct the termination of transcription by an RNA polymerase in the host cell.

The fungal cell may be modified with additional genetic constructs so as to enhance or reduce the expression and secretion of one or more homologous or heterologous proteins. For example, the fungal cell may be modified so as to over express a beta-glucosidase enzyme according to U.S. Pat. No. 6,015,703. The host cell may also be modified so as to produce an optimized blend of cellulase components and accessory components according to co-pending U.S. Publication No. US 2008/0057541 A1 and U.S. Patent Application No. 60/969,046. For example, the fungal cell may be modified with one or more genetic constructs comprising a gene encoding a cellulase enzyme operably linked to a promoter regulated by a Xyr1 transcription factor, such as a promoter from a cellulase or xylanase gene. The practice of the present invention is not limited by whether the additional genetic constructs directing the expression and secretion of the one or more homologous or heterologous proteins have been introduced previously to, simultaneously with, or subsequently to the modification that results in the overexpression of a Xyr1 or Xyr1 equivalent transcription factor.

Such genetic constructs that encode for the expression and secretion of a protein other than a Xyr1 or Xyr1 equivalent transcription factor, further comprise a secretion signal sequence. As used herein, a “secretion signal sequence” is a nucleic acid sequence encoding a peptide sequence present at the amino terminus of a secreted protein that directs entry of the protein into the endoplasmic reticulum (ER); the secretion signal may subsequently be cleaved from the mature secreted protein by a signal peptidase.

The modified host filamentous fungus used in the fermentation process of the present invention may be partially or completely deficient in the production of one or more hemicellulase enzymes such as xylanases, beta-xylosidases, arabinofuranosidases, mananases, alpha-glucuronidases, acetylxylan esterases, or a combination thereof. The modified host filamentous fungus additionally overexpresses a Xyr1 or Xyr1 equivalent transcription factor. However, it should be understood that the modified host filamentous fungus may be made partially or completely deficient in the expression of one or more hemicellulase enzymes previous to, simultaneous with, or subsequent to the modification that results in the overexpression of the Xyr1 or Xyr1 equivalent transcription factor.

By “partially or completely deficient in expressing one or more hemicellulase enzyme”, it is meant that the cellulase mixture secreted by the modified host filamentous fungus exhibits from about a 50% to about a 100% decrease in the relative proportion of at least one hemicellulase component as compared to relative proportion of the same hemicellulase component in a cellulase mixture produced by a corresponding hemicellulase deficient parental filamentous fungus when grown under identical conditions of medium composition, temperature, pH, cell density and age of culture. For example, the modified host filamentous fungus may exhibit a 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% decrease in the relative proportion of one or more hemicellulase enzyme as to relative proportion of the same hemicellulase component in a cellulase mixture produced by the corresponding hemicellulase deficient parental filamentous fungus when grown under identical conditions of medium composition, temperature, pH, cell density and age of culture.

When used in the context of determining the proportion of a hemicellulase enzyme in a cellulase mixture, a “hemicellulase deficient parental filamentous fungus” is a filamentous fungus that has not been genetically modified so as to exhibit a partial or complete deficiency in expressing the same one or more hemicellulase enzymes of whose expression the modified host filamentous fungus has been made to be partially or completely deficient.

Partial or complete deficiency in the expression of one or more hemicellulase enzymes can be achieved in a number of different ways known to one of ordinary skill in the art. For example, mutations may be introduced into one or more hemicellulase genes (insertion, deletion, or both) in the modified host filamentous fungus. In a non-limiting example, the modified host filamentous fungus contains deletion of the gene encoding either xylanase 2 or beta-xylosidase 1, or a double deletion of both.

Partial or complete deficiency in the expression of one or more hemicellulase enzymes may also be achieved by modifying the expression or function of a functional hemicellulase-specific transcriptional regulator(s). In the case of positive regulators or activators, the encoding gene sequence may be deleted or altered to as to produce a regulator with reduced activity. In the case of negative regulators or repressors, the encoding gene may be overexpressed or altered so as to produce a regulator with enhanced activity. For example, the coding sequence(s) of hemicellulase-specific transcriptional regulator gene(s) may by modified by insertion, deletion or both and/or the gene(s) encoding the hemicellulase-specific transcriptional regulator may also contain amino acid substitutions which modify protein function so as to reduce or enhance its DNA-binding activity, its interaction with other transcriptional regulators, its nuclear localization and the like.

Deleting a nucleic acid sequence may be achieved by engineering a construct that includes sequences from the target nucleic acid sequence itself into the construct, but in altered form. After transformation of the construct into the expression host, recombination then occurs with the altered target nucleic acid sequence, resulting in the insertion of the altered sequence to disrupt the native nucleic acid sequence. With its sequence interrupted, the altered gene in most cases will be translated into a nonfunctional protein, or not translated at all. An example of a method that may be used to delete a target nucleic acid sequence from a host cell include, but are not limited to, methods described in U.S. Pat. No. 5,298,405, which is incorporated herein by reference.

Hemicellulase deficiency may also be achieved by chemical or physical (for example UV) mutagenesis and selection of non-hemicellulase producing cells. In addition, the hemicellulase deficient cells may be isolated as a result of naturally occurring spontaneous mutations or inherited hemicellulase gene silencing.

A genetic construct may contain additional sequences between the various nucleic acid elements as described herein. These sequences, which may be natural or synthetic, may result in the addition of one or more of the amino acids to the protein encoded by the construct. The practice of the invention is not constrained by the presence of additional DNA sequences between the various nucleic acid elements of the genetic constructs present in the host cell.

The practice of the present invention is not constrained by the method of introducing the genetic constructs into the host cell. Methods of introducing the DNA construct into a host cell are familiar to those skilled in the art and include, but are not limited to, calcium chloride treatment of bacterial cells or fungal protoplasts to weaken the cell membranes, addition of polyethylene glycol to allow for fusion of cell membranes, depolarization of cell membranes by electroporation, or shooting the DNA through the cell wall and membranes via microprojectile bombardment with a particle gun.

Culture Medium

In the fermentation process of the present invention, the culture medium comprises a carbon source, a nitrogen source (either or both inorganic and organic in nature), and other essential minerals and nutrients as known by one of skill in the art. Organic nitrogen sources such as amino acids and peptides may also be utilized as sources of carbon; however, these organic nitrogen sources are not included in the calculation of carbon source supplied to the host cell during the fermentation process.

In a first embodiment, the carbon source supplied to the fungal cells in the fermentation process of the present invention comprises hemicellulose-derived carbohydrate (HDC). As used herein, the term hemicellulose-derived carbohydrate or HDC refers to one or more oligo-, di- or mono-saccharide that may be released by the chemical or enzymatic depolymerization of hemicellulose and which can be utilized by the host microbe for growth, enzyme production or both. Non-limiting examples of HDC include xylo-oligosaccharides, arabinoxylo-oligosaccharides, D-xylose, xylobiose, L-arabinose, D-mannose D-galactose and combinations thereof. For example, the HDC contains D-xylose and/or L-arabinose. The HDC represents from about 60 wt % to about 100 wt % of the carbon source fed to the fungal cells during the fermentation process. For example, the HDC may represent 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, 99 or 100 wt % or any amount therebetween, of the carbon sources fed to the fungal cells during the fermentation process. For example, the HDC may represent from about 80% to about 100% of the carbon source fed to the fungal cells during the fermentation process.

In a second embodiment, the carbon source supplied to the fungal cells in the fermentation process of the present invention comprises hemicellulose-derived sugar alcohol (HDSA), glycerol and/or glucose. As used herein, the term hemicellulose-derived sugar alcohol or HDSA refers to one or more sugar alcohols that may be derived from oligo-, di- or mono-saccharide released by the chemical or enzymatic depolymerization of hemicellulose and which can be utilized by the host microbe for growth, enzyme production or both. Non-limiting examples of HDSA include xylitol, mannitol, arabinitol, galactictol and combinations thereof. Preferably, the HDSA is xylitol or arabinitol. The HDSA represents from about 25 wt % to about 100 wt % of the carbon source fed to the fungal cells during the fermentation process. For example, the HDSA may represent 25, 30, 40, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, 99 or 100 wt % or any amount therebetween, of the carbon sources fed to the fungal cells during the fermentation process. For example, the HDC may represent from about 80% to about 100% of the carbon source fed to the fungal cells during the fermentation process. In addition to HDSA, the carbon source also contains about 0 wt % of a cellulase-inducing carbohydrate and from about 0 wt % to about 75 wt % glucose, glycerol or a combination thereof.

In addition to HDC or HDSA, the carbon source supplied to the fermentation process of the present invention also comprises from about 0 to about 3 wt %, or any amount therebetween, of a cellulose-inducing carbohydrate (CIC). As used herein, the term cellulose-inducing carbohydrate or CIC refers to one or more oligo- or di-saccharide that leads to the induction of cellulase production by the host cell. By induction, it is meant the switching on of the expression of one or more cellulase genes in response to the CIC. Non-limiting examples of cellulase-inducing carbohydrates include cellulose, lactose, cellobiose, sophorose, gentiobiose, and a combination thereof. Cellulase-inducing carbohydrate (CIC) may be produced by enzymatic conversion of cellulose with one or more cellulase enzymes to beta-linked glucose dimers. Alternatively, a high concentration glucose syrup can be condensed chemically or enzymatically to form mixtures of glucose dimers. For example, the condensation reaction to convert glucose to CIC may be catalyzed by dilute acid and performed at temperatures above 120-150° C., or by beta-glucosidase or cellulase enzymes at more moderate temperatures of about 40-70° C. (U.S. Publication No. US2004/0121446A1).

In addition to HDC and CIC, from about 0.1 to about 40 wt %, or any amount therebetween, of the carbon source supplied to the host cell during the fermentation process may comprise one or more of glucose, glycerol, sugar alcohols (such as xylitol or arabinitol), organic acids (such as acetic acid or glucuronic acid) or other carbon sources that can be utilized by the host cell. For example, from about 0.1, 0.2, 0.5, 0.8, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 7.0, 8.0, 10.0, 15, 20, 25, 30, 35, 40%, or any amount therebetween, of the total carbon supplied to the host cell during the fermentation process may comprise one or more of glucose, glycerol, sugar alcohols (such as xylitol or arabinitol), organic acids (such as acetic acid or glucuronic acid) or other carbon sources that can be utilized by the host cell.

One of skill in the art is aware that other nutrients, vitamins and minerals can be added to the fermentation media to improve growth and enzyme production of the host cell. These other media components may be added prior to, simultaneously with or after inoculation of the culture with the host cell.

Producing Cellulase Mixtures

Cellulase mixtures are typically produced by subjecting an actively growing fungal culture to media (solid or liquid) containing little or no glucose and a cellulase-inducing carbohydrate, as well as other nutrients required for cell growth, at temperatures and pH suitable for the host cell. In the fermentation process of the present invention, cellulase mixtures are produced by subjecting an actively growing culture of a modified host filamentous fungus overexpressing a Xyr1 to media (solid or liquid) a carbon source containing from about 60 wt % to about 100 wt % hemicellulose-derived carbohydrate and from about 0 wt % to about 3 wt % of a cellulase-inducing carbohydrate or in a medium comprising a carbon source containing from about 25 wt % to about 100 wt % of a hemicellulose-derived sugar alcohol, about 0% cellulase-inducing carbohydrate and from about 0 wt % to 75 wt % glucose, glycerol or a combination thereof

Expression of cellulases may be detected at the level of transcription by techniques known to those of ordinary skill in the art, including, but not limited to, Northern blot hybridization or quantitative real time PCT (qRT-PCR; see Example 1.3). Expression of the cellulase protein may be detected by several methods known to those of skill in the art including enzyme activity assays or protein immunodetection. Non-limiting examples of activity and immunodetection methods for cellulase mixtures are provided in Example 7.

Submerged liquid fermentations of Trichoderma and related filamentous fungi are typically conducted as a batch, fed-batch or continuous process. In a batch process, all the necessary materials, with the exception of oxygen for aerobic processes, are placed in a reactor at the start of the operation and the fermentation is allowed to proceed until completion, at which point the product is harvested. In a batch fermentation, the carbon source may be added to the fermentation medium prior to or simultaneously with inoculation.

In a fed-batch process, the culture is fed continuously or sequentially with one or more media components with the removal of the culture fluid. In a continuous process, fresh medium is supplied and culture fluid is removed continuously at volumetrically equal rates to maintain the culture at a steady growth rate. In the cases of fed-batch or continuous operations, the carbon source may also be supplied continuously or intermittently during the fermentation process. Preferably, the feed rate is between 0.2 and 2.5 g carbon/L of culture/h, or any amount therebetween. More preferably, the feed rate is between 0.4 and 1.6 g carbon/L of culture/h, or any amount therebetween.

The fermentation process of the present invention may be carried at a temperature from about 20° C. to about 35° C., or any temperature therebetween, for example from about 25° C. to about 30° C., or any temperature therebetween, or from 20, 22, 25, 26, 27, 28, 29, 30, 32, 35° C., or any temperature therebetween.

The fermentation process of the present invention may be carried out at a pH from about 3.0 to 6.5, or any pH therebetween, for example from about pH 3.5 to pH 5.5, or any pH therebetween, for example from about pH 3.0, 3.2, 3.4, 3.5, 3.7, 3.8, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.2, 5.4, 5.5, 5.7, 5.8, 6.0, 6.2, 6.5 or any pH therebetween.

The fermentation process of the present invention may be carried out over a period of 3-30 days, or any amount therebetween, for example between 3 and 10 days, or any amount therebetween, between 4 and 8 days, or any amount therebetween, or from 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 days, or any amount therebetween.

The fermentation process of the present invention may be performed in cultures of at least 1 litre, for example from about 1 to about 400,000 liters, or any amount therebetween, for example, 10 to about 400,000 litres, or any amount therebetween, 1,000 to about 200,000 litres, or any amount therebetween, or 10,000 to about 200,000 litres, or any amount therebetween, or from about 1, 10, 50, 100, 200, 400, 600, 800, 1000, 2000, 4000, 6000, 8000 10,000, 15,000, 20,000, 25,000, 30,000, 35,000, 40,000, 45,000, 50,000, 55,000, 60,000, 65,000, 70,000, 75,000, 80,000, 85,000, 90,000, 95,000, 100,000, 150,000, 200,000, 300,000, 400,000 litres in volume, or any amount therebetween.

The fermentation process of the present invention may be performed aerobically, in the presence of oxygen, or anaerobically, in the absence of oxygen. Preferably, the process is performed aerobically.

Following fermentation, the cellulase mixture thus produced may be used directly, or the cellulase mixture may be separated from the fungal cells, for example by filtration or centrifiguation. Low molecular solutes such as unconsumed components of the fermentation medium may be removed by ultrafiltration. The cellulase mixture maybe concentrated, for example, by evaporation, precipitation, sedimentation or filtration. Chemicals such as glycerol, sucrose, sorbitol and the like may be added to stabilize the cellulase enzyme. Other chemicals, such as sodium benzoate or potassium sorbate, may be added to the cellulase mixture to prevent growth of microbial contaminants.

The fermentation process of the present invention may produce a cellulase mixture containing at least about 2-fold more secreted protein than a corresponding process in which the carbon source contains only HDC and is performed using a fungal strain that has not been modified or selected for increased expression of a Xyr1 or Xyr1 equivalent transcription factor. For example the process described herein may produce 2.5 to about 10 fold more, or any amount therebetween, for example about 2.5, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, 4.2, 4.4, 4.6, 4.8, 5.0, 5.2, 5.4, 5.6, 5.8, 6.0, 6.2, 6.4, 6.6, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0, 8.2, 8.4, 8.6, 8.8, 9.0, 9.2, 9.4, 9.6, 9.8, 10 fold more secreted protein, or any amount therebetween or more than 10 fold more secreted protein, than a corresponding process in which the carbon source contains only HDC and is performed using a fungal strain that has not been modified or selected for increased expression of a Xyr1 or Xyr1 equivalent transcription factor. Thus, the fermentation process may be characterized by having from about a 2-fold, for example from about a 5-fold, or any amount therebetween, increase in specific productivity (q_(p)) in terms of mg secreted cellulase produced/g biomass/h than a corresponding process in which the carbon source contains only HDC and is performed using a fungal strain that has not been modified or selected for increased expression of a Xyr1 or Xyr1 equivalent transcription factor. An increase in specific productivity of protein production in the presence of varying amount of HDC, cellulose inducing carbohydrate (CIC), or both HDC and CIC as described herein, is shown in Table 2.

TABLE 2 Production of protein and fungal cells from submerged liquid cultures of parental and modified filamentous fungi on various carbon sources Fermentation profile Final Final Strain Information and Fermentation Feed protein, biomass, Avg qp, Max qp, Ferm# Strain xyr1 xyn2 Fermentation Feed g/L g/L mg/g/h mg/g/h 2404 P285-6 wt wt H2 37.44 14.29 22.42 41.68 3964 P285-6 wt wt 32.42 13.87 19.46 43.66 3796 P692B xyr1+ wt 30.41 14.14 20.62 34.97 3963 P692B xyr1+ wt 34.31 13.77 22.98 45.74 3685 P285-6 wt wt 100% Xylose 5.93 38.79 3.05 7.22 3951 P285-6 wt wt 8.24 37.34 3.07 5.35 3684 P692B xyr1+ wt 35.20 16.00 21.60 29.00 3950 P692B xyr1+ wt 35.03 14.70 20.55 38.04 4254 P692A xyr1+ wt 28.21 22.31 13.71 23.32 4000 P285-6 wt wt 100% Arabinose 9.17 35.01 3.13 6.96 3735 P285-6 wt wt 7.91 34.55 1.73 7.75 3734 P692B xyr1+ wt 31.87 25.60 11.67 16.75 3980 P692B xyr1+ wt 21.78 27.25 10.21 15.18 4217 P285-6 wt wt 50% glucose/ 3.34 37.48 1.37 5.54 4042 P692B xyr1+ wt 25% glycerol/ 29.11 23.26 15.38 26.61 4086 P692B xyr1+ wt 25% xylitol 27.8 22.08 13.58 20.49 4218 P285-6 wt wt 50% glucose/ 6.07 32.67 2.53 5.43 4043 P692B xyr1+ wt 25% glycerol/ 32.65 19.74 15.84 23.95 4087 P692B xyr1+ wt 25% xylose 27.31 25.15 12.78 23.05 4279 RutC30 wt wt H2 14.97 8.46 7.35 13.55 4280 RutC30-R3 xyr1+ wt 27.50 20.35 12.14 16.79 4073 RutC30 wt wt 100% Xylose 2.50 55.33 1.06 3.11 4074 RutC30-R3 xyr1+ wt 35.13 31.70 13.44 21.05 4255 RutC30-R3 xyr1+ wt 37.38 26.57 15.45 23.33 4258 M2C38 wt wt 7.66 29.86 3.51 8.36 4101 P491P wt xyn2− 6.11 40.35 2.39 6.81 4120 P1194E xyr1+ xyn2− 25.15 28.11 10.95 19.74 4121 P1194F xyr1+ xyn2− 24.13 27.00 10.55 19.92 4122 P1197B xyr1+ xyn2− 22.92 27.51 9.95 18.54 4403 RutC30-R3 xyr1+ wt 50% glucose/ 15.17 11.61 6.04 12.05 25% glycerol/ 25% xylitol 4404 P692B xyr1+ wt 99% Xylose/1% J1 27.13 7.60 15.72 29.61 4417 P692B xyr1+ wt 97% Xylose/3% J1 39.47 13.84 20.89 29.91 ^(a)CIC for these fermentations was inducing cocktail comprising, as a function of total carbohydrate, 56% gentiobiose, 14% sophorose, 6% cellobiose, 10% trehalose, 6% maltotriose, 4% glucose and 14% other carbohydrates

Cellulase Mixtures

The fermentation process of the present invention produces a cellulase mixture. As used herein, a “cellulase mixture” is a mixture comprising cellulase components, hemicellulase components and other protein secreted by the modified host filamentous fungus during the fermentation process. The cellulase mixture produced by the fermentation process comprises from about 40 to about 100 wt % cellulase components relative to the total protein present in the cellulase mixture. For example, cellulase components may represent from about 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 wt % of the total protein in the cellulase mixture, or any amount therebetween. The relative proportion of cellulase components in cellulase mixtures produced by modified host filamentous fungi using the fermentation process of the present invention are shown in Table 3.

As used herein, the term “cellulase component” or “cellulase components” includes endoglucanases (E.C. 3.2.1.4), cellobiohydrolases (E.C. 3.2.1.91), beta-glucosidase (E.C. 3.2.1.21), and mixtures thereof. The terms “cellulase component” or “cellulase components” also includes other proteins, such as swollenins, that are involved in or enhance the enzymatic degradation of cellulose. It should be understood that the practice of the present invention is not limited by the identity of the cellulase component(s) in the cellulase mixture. Cellulase components are part of a broader family of enzymes referred to as glycosyl hydrolases. Glycosyl hydrolases are divided into different families and are listed in the database for Carbohydrate-Active Enzymes (Coutinho, P. M. & Henrissat, B., 1999; also see: afmb.cnrs-mrs.fr/CAZY/). This database and nomenclature are familiar to those skilled in the art. Cellulase components are most commonly found as members of glycosyl hydrolase families 1, 3, 5, 6, 7, 12, 45 or 61. As it relates to the native cellulase mixture produced by T. reesei, the term “cellulase component(s)” refers to some or all of the following: cellobiohydrolase 1 (Cel7A), cellobiohydrolase 2 (Cel6A), endoglucanase 1 (Cel7B), endoglucanase 2 (Cel5A), endoglucanase 3 (Cel12A), endoglucanase 4 (Cel61A), endoglucanase 5 (Cel45A), beta-glucosidase 1 (Cel3A) and beta-glucosidase 2 (Cel3B), CipI and Swollenin.

Enzymes involved in the degradation hemicelluloses are referred to herein as “hemicellulases” or “hemicellulase components” (reviewed in Saha, B.C. (2003). Hemicellulases include, but are not limited to, endo-xylanases (E.C. 3.2.1.8), beta-xylosidases (E.C. 3.2.1.37), alpha-arabinofuranosidases (E.C. 3.2.1.55), alpha-glucuronidases (E.C. 3.2.1.139), acetylxylan esterases (E.C. 3.1.1.72), ferulic acid esterases (E.C. 3.1.1.73), beta-mannanases (E.C. 3.2.1.78), and beta-mannosidases (3.2.1.15). Xylans are the most abundant hemicelluloses. The term “xylanases” or “xylanase components” as used herein refers to enzymes that have endo-xylanase, exo-xylanase or beta-xylosidase activity. Xylanases may belong to glycosyl hydrolase families 3, 5, 10 and 11. As it relates to the native cellulase mixture produced by T. reesei, the term “xylanase” or “xylanase components” refers to some or all of the following enzymes from Trichoderma reesei: beta-xylosidase 1 (Bxl1), beta-xylosidase 2 (Bx12), xylanase 1 (Xyn1), xylanase 2 (Xyn2), xylanase 3 (Xyn3) and xylanase 4 (Xyn4).

TABLE 3 Composition of cellulase mixtures secreted from submerged liquid cultures of parental (and modified host filamentous fungi on various carbon sources. Composition of Secreted Enzyme (wt % total protein) Strain Information and Fermentation Feed Cellu- Xyla- Beta- Relative Ferm# Strain xyr1 xyn2 Carbon Source lase ^(a) nase ^(b) xylosidase ^(c) Activity ^(d) 2404 P285-6 wt wt 65% glucose + 69.4 — Nd 1.00 ± 0.02 3964 P285-6 wt wt 35% CIC 71.9 — Nd 0.98 ± 0.03 3796 P692B xyr1+ wt 80.6 — Nd 1.09 ± 0.03 3963 P692B xyr1+ wt 64.8 — Nd 1.05 ± 0.03 3685 P285-6 wt wt 100% xylose 14.3 25.4 31.9 0.12 ± 0.02 3951 P285-6 wt wt 11.8 27.4 34.0 0.07 ± 0.03 3684 P692B xyr1+ wt 54.4 21.3 1.8 0.55 ± 0.02 3950 P692B xyr1+ wt 49.4 23.9 1.6 0.68 ± 0.04 4254 P692A xyr1+ wt 46.6 18.4 1.9 0.39 ± 0.03 4000 P285-6 wt wt 100% arabinose 20.6 27.2 12.3 0.21 ± 0.03 3735 P285-6 wt wt 28.3 35.6 10.6 0.23 ± 0.03 3734 P692B xyr1+ wt 47.9 14.4 5.8 0.46 ± 0.03 3980 P692B xyr1+ wt 40.6 23.5 2.6 0.57 ± 0.04 4217 P285-6 wt wt 25% xylitol/ 58.8 5.6 3.1 0.43 ± 0.03 4042 P692B xyr1+ wt 50% glucose/ 64.8 4.1 0.4 0.74 ± 0.06 4086 P692B xyr1+ wt 25% glycerol 64.1 4.7 0.7 0.71 ± 0.03 4218 P285-6 wt wt 25% xylose/ 29.3 30.5 20.7 0.21 ± 0.04 4043 P692B xyr1+ wt 50% glucose/ 45.7 16.3 2.1 0.44 ± 0.07 4087 P692B xyr1+ wt 25% glycerol 39.8 13.1 4.5 0.40 ± 0.03 4279 RutC30 wt wt 65% glucose + 86.6 1.4 Nd 1.00 ± 0.08 4280 RutC30-R3 xyr1+ wt 35% CIC 85.5 — Nd 1.12 ± 0.08 4073 RutC30 wt wt 100% xylose 18.5 13.7 20.1 0.20 ± 0.06 4074 RutC30-R3 xyr1+ wt 52.9 6.4 1.7 1.36 ± 0.08 4255 RutC30-R3 xyr1+ wt 71.5 6.4 1.1 0.99 ± 0.04 4258 M2C38 wt wt 47.5 21.5 7.7 0.41 ± 0.06 4101 P491P wt xyn2− 29.5 14.6 20.0 0.38 ± 0.05 4120 P1194E xyr1+ xyn2− 62.6 10.9 4.0 0.84 ± 0.06 4121 P1194F xyr1+ xyn2− 58.6 10.2 4.5 0.78 ± 0.05 4122 P1197B xyr1+ xyn2− 59.0 11.0 4.1 0.74 ± 0.06 4403 RutC30-R3 xyr1+ wt 25% xylitol/ 82.3 1.1 — 1.22 ± 0.05 50% glucose/ 25% glycerol ^(a) CIC for these fermentations was inducing cocktail comprising, as a function of total carbohydrate, 56% gentiobiose, 14% sophorose, 6% cellobiose, 10% trehalose, 6% maltotriose, 4% glucose and 14% other carbohydrates ^(b) Ratio is based on results of ELISA determinations as described in Example 5.3. Ratio is the sum of the concentrations of the Cel7A, Cel7B, Cel6A and Cel5A cellulases to the sum of the concentration of the xyn1 and xyn2 xylanases, as shown in FIG. 12. ^(c) Relative hydrolysis activity on a pretreated lignocellulosic substrate as described in Example 5.4.

Hydrolysis of Cellulosic Substrates

The cellulase mixture produced using the fermentation process of the present invention is useful for the hydrolysis of cellulase or a cellulosic substrate. By the term “cellulosic substrate”, it is meant any substrate derived from plant biomass and comprising cellulose, including, but not limited to, pre-treated lignocellulosic feedstocks for the production of ethanol or other high value products, animal feeds, forestry waste products, such as pulp and wood chips, and textiles. The activity of the cellulase mixtures produced by the fermentation process of the present invention on pretreated lignocellulosic feedstock is presented in Table 3.

The cellulase enzyme produced by the fermentation process of the present invention may be used for the enzymatic hydrolysis of a “pretreated lignocellulosic feedstock”. A pretreated lignocellulosic feedstock is a material of plant origin that, prior to pretreatment, contains at least 20% cellulose (dry wt), more preferably greater than about 30% cellulose, even more preferably greater than 40% cellulose, and at least 10% lignin (dry wt), more typically at least 12% (dry wt) and that has been subjected to physical and/or chemical processes to make the fiber more accessible and/or receptive to the actions of cellulolytic enzymes. Non-limiting examples of pretreatment processes include chemical treatment of a lignocellulosic feedstock with sulfuric or sulfurous acid, or other acids; ammonia, lime, ammonium hydroxide, or other alkali; ethanol, butanol, or other organic solvents; or pressurized water (See U.S. Pat. Nos. 4,461,648, 5,916,780, 6,090,595, 6,043,392, 4,600,590, Weil et al., 1997, Appl. Biochem. Biotechnol. 681: 21-40, and Öhgren, K., et al., 2005, Appl. Biochem. Biotechnol. Spring (121-124): 1055-1067; which are incorporated herein by reference).

For example, the cellulosic substrate may be incubated with the cellulase enzyme produced using the methods described herein, at a concentration of from about 1 to about 200 g cellulose per L of reaction mixture, or any amount there between, for example from about 1, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, or any amount therebetween, and with a cellulase dosage of from about 0.1 to about 100 mg protein per g cellulose, or any amount therebetween, for example from about 0.1, 0.5, 1.0, 2.0, 5.0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 mg protein/g cellulose, or any amount therebetween. The reaction mixture may be incubated for from about 4 hours to about 120 hours, or any amount therebetween, at a temperature from about 30° to about 60° C., or any temperature therebetween, for example from about 30, 35, 40, 45, 50, 55, 60° C. or any temperature therebetween, and at a pH from about 3.5 to about 7.0, or any pH therebetween, for example a pH of about 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0 or any pH therebetween. Following incubation, the reaction products, including hemicellulose-derived carbohydrates, cellulase-inducing carbohydrates, glucose, and/or oligosaccarides can be used for further processing, for example as a substrate for producing ethanol, butanol, sugar alcohols, lactic acid, acetic acid, or the end products may be concentrated and purified using standard methods as known in the art.

In summary, the present invention provides highly productive fermentation processes that produce cellulase enzymes with low hemicellulase content useful for the hydrolysis of cellulosic substrates.

The above description is not intended to limit the claimed invention in any manner. Furthermore, the discussed combination of features might not be absolutely necessary for the inventive solution.

EXAMPLES Example 1 Host Strains for Cloning and Expression of Xyr1 Transcription Factor Example 1.1 Host Trichoderma Strains for the Overexpression of Xyr1 Transcription Factor

The host Trichoderma reesei strains used for the overexpression of xyr1 transcription factor are RutC30, P285-6aux and P491P6.

Strain RutC30 (ATCC #56765) was isolated as a high cellulase producing derivative of progenitor strain QM6A (Montenecourt and Eveleigh, 1979). Cellulase hyper-producing strains were generated from RutC30 by random mutation and/or selection. Strain M2C38 was isolated based on its ability to produce larger clearing zones than RutC30 on minimal media agar containing 1% acid swollen cellulose and 4 g L⁻¹ 2-deoxyglucose. Next, M2C38 was subjected to further random mutagenesis and strain BTR213 strain isolated by selection on lactose media containing 0.2 μg/mL carbendazim.

Strain P285-6aux is a derivative of strain BTR213 containing a deletion in the gene encoding endoglucanases 2 and also lacking the ability to grow on media lacking uridine. Deletion of the endoglucanases 2 gene was achieved by transformation of strain BTR213 with the p̂EG2-hph-TV3 vector shown in FIG. 1. The coding region of the cel5a gene in p̂EG2-hph-TV3 has been replaced by a hygromycin-resistance cassette in which the hygromycin phosphotransferase gene (hph) is operatively linked to the promoter of the T. reesei pgk gene and the transcriptional terminator of the T. reesei cellobiohydrolases 1 gene (as described in U.S. Pat. No. 6,015,703). The hygromycin-resistance cassette is flanked by approximately 2.8 kb and 2.4 kb of the endoglucanse 2 gene at the 5′ and 3′ ends, respectively, to enable homologous recombination within the endoglucanases 2 locus in the T. reesei genome. Strain BTR213 was transformed with p̂EG2-hph-TV3, that had been linearized by digestion with XbaI restriction endonuclease, using PEG-mediated protoplast transformation method as described in Example 4. Transformants were selected on PDA media containing 20 U/mL of hygromycin. Deletion of the endoglucanases 2 gene was confirmed by Southern hybridization using the endoglucanase 2 coding sequence as a probe (FIG. 1B). A pyr4 auxotroph of strain P285-6 (strain P285-6aux), deficient in uracil production, was isolated based on the ability to grow on minimal media agar supplemented with 5 mM uridine and 0.15% (w/v) of 5-fluoro-orotic acid.

Strain P491P6 is a derivative of strain M2C38 containing a deletion in the xylanase 2 gene and also lacking the ability to grow on media lacking uridine. Deletion of the xylanase 2 gene was achieved by transformation of strain M2C38aux5, a pyr4 auxotroph of M2C38 selected for the ability to grow on minimal media agar containing 5 mM uridine and 0.15% (w/v) 5-fluoro-orotic acid, with the pXBG2-pyr4-DR vector shown in FIG. 2. The coding region of the xylanase 2 gene in pXBG2-pyr4-DR has been replaced by a large insert comprising the T. reesei cel3a gene (encoding beta-glucosidase I) into which the N. crassa pyr4 gene flanked by Direct Repeats has been inserted. The direct repeat sequences were amplified by PCR using tetracycline gene as a template (671 bp-990 bp) and following primers: DR1-F GCGTGCTGCTAGCGCTATATGC (SEQ ID NO: 28), DR1-R GGCCTGGTACCATACCCACG (SEQ ID NO: 29), DR2-F GCGTGCTGGTACCGCTATATGC (SEQ ID NO: 30) and DR2-R GGCCTGCTAGCATACCCACG (SEQ ID NO: 31). The cel3A-pyr4 direct repeat cassette in pXBG2-pyr4-DR is flanked by approximately 2.1 kb and 1.9 kb of the xylanase 2 gene at the 5′ and 3′ ends, respectively, to enable homologous recombination within the xylanase 2 locus in the T. reesei genome. Strain M2C38aux5 was transformed with pXBG2-pyr4-DR that had been linearized with Cla 1 restriction enzyme using PEG-mediated protoplast transformation method as described in Example 4. Transformants were selected on minimal medium agar as described in Example 4. All stable transformants were screened for deletion of the xylanase 2 gene by PCR amplication from genomic DNA using primers complementary to the xylanase 2 coding (data not shown). To verify the inability to produce xylanase 2 protein, all transformants were grown in Trichoderma micro-culture media with xylose as described in Example 5.1. The total secreted protein (10 μg) was separated on 12% SDS-PAGE, transferred to PVDF membrane and immunoblotted using antibodies raised against xylanase 2. The absence of xyn2 specific band in the total secreted protein samples of some transformant strains confirmed successful deletion of xyn2 gene (FIG. 2B). A pyr4 auxotroph of strain P491P (strain P491P6) deficient in uracil production was isolated based on the ability to grow on minimal media agar supplemented with 5 mM uridine and 0.15% (w/v) of 5-fluoro-orotic acid

Example 2 Enzyme Production and Expression Levels of Transcriptional Regulators, Xyr1 and Ace1, in Trichoderma Fermentations on Different Feeds

T. reesei strain P59G was used for the assessment of protein, biomass production, q_(p) and the expression levels of cbh1 (cellobiohydrolase 1), xyr1 (xylanase regulator 1) and ace1 (activator of cellulase 1) grown in fed-batch fermentation on different carbon sources. Strain P59G is a genetically modified strain of strain BTR213 (described in Example 1) that produces and secretes high levels of the beta-glucosidase encoded by T. reesei bgl1 as described in U.S. Pat. No. 6,015,703.

Example 2.1 Fermentations on Pentose Sugars with CIC

Trichoderma spores from frozen (−80° C.) 15% glycerol stocks of strain P59G were inoculated onto standard 85 mm Petri plates containing potato dextrose agar (PDA). These plates were incubated at 28° C. for 3-5 days to achieve a confluent growth of fresh green spores. To prepare the inoculum for fermentation testing, spores from a single PDA plate were transferred to 2 L, baffled Erlenmeyer flask containing 750 mL of liquid Berkley media (pH 5.5) supplemented with 5.1 g/L of corn steep liquor powder and 10 g/L glucose. Flasks were incubated at 28° C. for 3 days using an orbital agitator (Model G-52 New Brunswick Scientific Co.) running at 100 rpm.

Berkley Media for Flasks Component g/L (NH₄)₂SO₄ 10.4 KH₂PO₄ 2.0 MgSO₄•7H₂O 0.31 CaCl₂•2H₂O 0.53 Dry Corn Steep Liquor 5.1 Glucose 10 Trace elements* 1 mL/L *Trace elements solution contains 5 g/L FeSO₄•7H₂O; 1.6 g/L MnSO₄•H₂O; 1.4 g/L ZnSO₄•7H_(2O)0.

The contents of an inoculum flask were transferred to a 14 L pilot scale fermentation vessel (Model MF114 New Brunswick Scientific Co.) set up with 10 L of Initial Pilot Media (pH 5.5). The vessel was run in batch mode until glucose in the media was depleted. At this point, the carbon source was added, on a continuous basis, from a stock that was 35.5% w/v of solids dissolved in water. Peristaltic pumps were used to deliver the carbon source at a feed at a rate of 0.4 grams of carbon per liter culture per hour. Operational parameters during both the batch and fed-batch portions of the run were: mixing by impeller agitation at 500 rpm, air sparging at 8 standard liters per minute, and a temperature of 28° C. Culture pH was maintained at 4.0-4.5 during batch growth and pH 3.5 during cellulase production using an automated controller connected to an online pH probe and a pump enabling the addition of a 10% ammonium hydroxide solution. Periodically, 100 mL samples of broth were drawn for biomass and protein analysis. The total fermentation time is typically between 96-144 hours.

Initial Media for Fed-Batch Fermentations Component g/L (NH₄)₂SO₄ 2.20 KH₂PO₄ 1.39 MgSO₄•7H₂O 0.70 CaCl₂•2H₂O 0.185 Dry Corn Steep Liquor 6.00 Glucose 13.00 Trace elements* 0.38 mL/L *Trace elements solution contains 5 g/L FeSO₄•7H₂O; 1.6 g/L MnSO₄•H₂O; 1.4 g/L ZnSO₄•7H₂O.

The biomass content of the culture broth was determined using aliquots of 5-10 mL that had been weighed, vacuum filtered through glass microfiber filters, and oven dried at 100° C. for 4 to 24 hours. The concentration of biomass was determined according to the equation below.

Biomass(g/L)=dry filter paper and cake (g)−filter mass (g)×broth density (g/mL)×1000 (mL/L) wet sample mass (g)

The protein concentration of culture filtrate was determined using the Bradford assay. Colour intensity changes in the Coomassie Brilliant Blue G-250 dye, that forms the basis of this assay, were quantified spectrophotometrically using absorbance measurements at 595 nm. The standard assay control used was a cellulase mixture of known composition and concentration. The specific productivity, q_(p), was expressed as mg protein produced per gram of biomass per hour of fermentation.

Trichoderma reesei P59G strain fermentation profiles on various carbon sources are shown in FIG. 1. As expected, the amount of total protein produced during 164 hrs on a cellulase-inducing cocktail (CIC) is significantly higher than that produced in fermentations on either xylose or arabinose with 2% cellobiose. In contrast, the production of biomass was significantly higher on pentose sugars and resulted in low specific productivity over the course of fermentation (Table 4). The production of cellulase on hemicellulose derived carbohydrate (HDC) can be improved by additions of 8-15% of CIC to the feed (Table 4).

TABLE 4 Protein and biomass production by T. reesei P59G on different feed type. Strain Carbon source Protein, Biomass, Average q_(p), Max q_(p), Strain Carbon source g/L g/L mg/g/L mg/g/L P59G 65% Glucose/ 36.95 18.49 21.74 41.77 35% CIC^(a) P59G 98% Xylose + 15.84 35.65 6.47 11.16 2% cellobiose^(b) P59G 98% Arabinose + 10.71 32.94 4.44 11.01 2% cellbiose^(b) ^(a)average from five fermentations ^(b)average from two fermentations

Example 2.2 Expression Levels of Xyr1, Ace1 and Cel7a on Different Carbon Sources

Biomass samples were obtained from the above fermentations at the time point of 72 hrs after cellulase induction. The fermentation samples were filtered through GF/A microfiber paper, washed with sterile water and frozen in liquid nitrogen. Frozen mycelia was crushed by grinding in liquid nitrogen and total RNA was extracted using the procedure outlined in Strategene RNA Isolation Kit (VWR Cat. # CA99900-134). RNA was quantified using a conversion of OD_(260 nm)=1.0 representing a concentration of 40 μg/mL. First strand cDNA was prepared using exactly 10 μg of total RNA from each transformant sample. RNA was mixed with 1.5 μL of 100 μM AncT primer (Invtrogen), 2 μL of 25 mM dNTP (each dNTP 6.25 mM) and made up to 25 μL with RNase and DNAse free water from GIBCO. The RNA mixture was heated at 65° C. for 5 minutes and then quick cooled in an ice bath for 2 minutes. To this mixture, 8 μL of 5× first strand Buffer (Invitrogen), 4 μL of 0.1M DTT (Invtrogen) and 1 μL of RNasein (Invitrogen) were added. The tubes were mixed and incubated at 42° C. for 2 minutes. Following this, 2 μL of SuperScriptII (Invitrogen) was added. The synthesis reaction was continued at 42° C. for 60 minutes for all samples. First strand cDNA was stored at −20° C.

The expression levels of genes encoding transcriptional regulators xyr1 and ace1 and their target cbh1 gene were determined by quantitative real-time PCR (qRT-PCR) using the Strategene MX3000P qRT-PCR system. All qRT-PCR reagents, except for the amplicon-specific primers, were purchased from Stratagene and used according to the manufacturer's instructions. Measurement of transcript levels was determined using the standard curve method. Standard curves were constructed for a constitutively expressed reference gene encoding nuclear transport factor 2 (Ntf-2) and for each of the xyr1, ace1 and cel7a amplicons using the primers indicated in Table 5 (SEQ ID 1 to 8). For generation of standard curves, equal aliquots of all collected cDNA samples were pooled, diluted 1:10, 1:100 and 1:1000 in sterile water and used for qRT-PCR as follows. To determine the relative transcript level of each gene cDNA, diluted samples were further diluted 1:20 and 2 μL aliquoted in triplicate into a 96-well qRT-PCR array micro-well plate. To each well, 18 μL of SYBR Green Master mix containing: 2×Brilliant SYBRGreen (10 μL), 1/500 dilution (0.75 μL) of ROX reference dye, 10 pmol containing equal amount of forward and reverse primers (1 μL) and 6.25 μL of GIBCO water were added. The PCR profile consisted of the following steps: I) 1 cycle of 15 min at 25° C., 10 min at 95° C.; II) 40 cycles of 30 sec at 95° C.; 20 sec at 55° C.; 20 sec at 72° C.; III) 1 cycle of 1 min at 95° C.; 30 sec at 55° C.; 30 sec at 95° C. Analysis of the data was performed as described in the Stratagene MX3000P manual for converting the fractional cycle at which exponential produced is reliably detected (Ct) to copy number. Standard curves were plotted for each gene to measure the copy number. These values were then normalized to the reference gene Ntf-2. The final value is the relative expression level of the target gene in relation to reference gene.

TABLE 5 List of primers used for qRT-PCR: SEQ ID Primer name Primer sequence 1 Ntf2F ACAGAGTTGGCATTGTAGACAGCG 2 Ntf2R CGAGTAAAGCACACAAACCGCCAA 3 Xyr1F AGCCAGATTCTCGAGTTTGACCCT 4 Xyr1R GCAAGCTTCGTGTGCCCTAACAAT 5 Ace1F AGAAGGAAATGGACCGCCACATCA 6 Ace1R AGTTCGACTCACGCTTCGACTTGT 7 Ce17aQ1F TACTCTGGCAACGAAGCTCAACGAT 8 Ce17aQ1R GCCACAGCATGTTGGCGTAGTAA

The expression levels of cbh1 gene on 98% xylose+2% cellobiose or 98% arabinase+2% cellobiose are lower than that on 65% glucose+35% CIC (FIG. 3). This correlates with protein production profiles (Table 4) and the expression levels of transcriptional activator Xyr1 encoding gene (FIG. 3). In contrast, the transcript levels of the negative transcriptional regulator ace1 are independent of carbon source supplied to the fermentation (FIG. 3). Without wishing to be bound by theory, it is possible that the lower levels of positive transcriptional regulator Xyr1 is the rate limiting factor which results in lower cellulase and overall protein production on HDC.

Example 3 Cloning of Trichoderma reesei Xyr1 Gene Example 3.1 Trichoderma reesei Genomic DNA Isolation and Amplification of Xyr1

For genomic DNA isolation, T. reesei spores collected from a Potato Dextrose Agar (PDA) plate were inoculated in 50 mL of Potato Dextrose Broth (PDB) (Difco). The cultures were shaken at 200 rpm for 2-3 days at 28° C. The mycelium was filtered onto a glass fiber circles (GFA) (Fisher Cat. #09-804-424) and washed with cold, deionized water. The fungal cakes were frozen in liquid nitrogen and crushed into a powder with a pre-chilled mortar and pestle; 0.5 g of powdered biomass was resuspended in 5 mL of buffer containing 100 mM Tris, 50 mM EDTA, pH 7.5 and 1% sodium dodecyl sulphate (SDS). The lysate was centrifuged (5000 g for 20 mM at 4° C.) to pellet cell debris. The supernatant was extracted with 1 volume of TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) saturated phenol followed by extraction with 1 volume of buffer-saturated phenol:chloroform:isoamyl alcohol (25:24:1). Genomic DNA was precipitated from the solution by adding 0.1 volumes of 3 M sodium acetate, pH 5.2 and 2.5 volumes of cold 95% ethanol. After incubating for at least 1 h at −20° C., the DNA was pelleted by centrifugation (5000 g for 20 mM at 4° C.), rinsed with 10 mL 70% ethanol, air-dried and resuspended in 1 mL of TE buffer. The RNA was digested by the addition of Ribonuclease A (Sigma-Aldrich) (final concentration of 0.1 mg/mL) and incubation at 37° C. for 1 hour. Ribonuclease was removed by extracting with 1 volume of buffer-saturated phenol and 1 volume of buffer-saturated phenol:chloroform:isoamyl alcohol (25:24:1). The DNA was precipitated with 0.1 volumes of 3 M sodium acetate, pH 5.2 and 2.5 volumes of cold 95% ethanol, pelleted by centrifugation, rinsed with 70% ethanol, air-dried and resuspended in 50 μL of TE buffer. The concentration of DNA was determined by measuring the absorbance of the solution at 260 nm (p. C1 in Sambrook et al., 1989).

A DNA fragment comprising the xyr1 coding sequence and native terminator (SEQ ID NO: 23) was amplified from T. reesei genomic DNA using Platinum® Taq DNA polymerase (Invitrogen) and following primers: forward —CH25 CATATGTTGTCCAATCCTCTCCG (SEQ ID NO: 9) and reverse —CH26 GCGGCCGCGGTACCTACAGCCATGCTCATCGTGC (SEQ ID NO: 10). Restriction sites for NdeI and KpnI-NotI were added at the 5′ and 3′ ends of the xyr1 coding sequence and native terminator fragment, respectively. The PCR was performed according to the enzyme manufacturer's protocol with a primer annealing temperature of 60° C. and 4 min extension time for 30 cycles. The PCR reaction products were then run on 1% agarose TAE gel and a 3.5 Kb amplicon was gel extracted using Wizard SV Gel and PCR Clean-up System (Promega).

Example 3.2 Construction of the Plasmids

The PCR product containing the xyr1 coding region (SEQ ID NO: 24) was ligated into the pGEM®-T Easy Vector (Promega) generating pGEM-xyr1-t. The inducible beta-xylosidase 1 promoter (Pbxl1, SEQ ID NO: 26) was amplified from T. reesei genomic DNA using Platinum® Taq DNA polymerase (Invitrogen) and the following primers: forward —CH27 5′-GGTACCCAATTGAGAGCTTGTCTGCCTTGATTACCATCC-3′ (SEQ ID NO:13) and reverse —CH25′-AAGCTTGCGGCCGCCATATGCGTCCGGCTGTCCTTCAATGG-3′ (SEQ ID NO:14). These primers also added KpnI and NdeI-NotI-HindIII restriction sites were introduced at the 5′ and 3′ ends, respectively, of the amplified promoter fragments. The PCR reaction was performed according to the enzyme manufacturer's recommendations with a primer annealing temperature of 51.5° C. and 2.5 min extension time for 30 cycles. The 1.5 kb Pbxl PCR product of was purified using the Wizard SV Gel and PCR clean-up System (Promega) and cloned into the pGEM®-T Easy Vector (Promega) resulting in the generation of vector pGEM-Pbxl1. After digestion of this vector with KpnI and HindIII restriction enzymes, the Pbxl1 promoter fragment was gel extracted using the Wizard SV Gel and PCR clean-up System (Promega) and cloned into the corresponding sites of pUC119 vector generating pUC119-Pbxl1 plasmid. The pGEM-xyr1-t plasmid was digested with NdeI and KpnI restriction enzymes, the xyr1 fragment was separated by agarose gel eletrophoresis and gel extracted using Wizard SV Gel and PCR Clean-up System (Promega). The fragment was cloned into corresponding sites of pUC119-Pbxl1 plasmid generating pUC119-Pbxl1-xyr1-t plasmid.

The selectable marker cassette conferring resistance to hygromycin was isolated from pHPT136 (described in U.S. Pat. No. 6,015,703) with XhoI and BglII restriction enzymes. The Ppgk-hph-Tcbh1 fragment was gel purified and ligated into XhoI and BamHI sites of pSP72 vector generating pSP-hph vector. The pUC119-Pbxl-xyr1-t was digested with the KpnI restriction enzyme and ˜5.0 kb fragment containing xyr1 expression cassette was gel purified and ligated into KpnI site of pSP-hph vector to generate the pSP-bxl:xyr1-hph T. reesei transformation vector (FIG. 4A).

A pPbxl:xyr1-pyr4 T. reesei transformation vector was generated as follow. Plasmid pNcBgl-NSN(r)* (described in U.S. Pat. No. 7,456,005) containing the Neurospora crassa pyr4 gene was partially digested with KpnI restriction enzyme. The 6.2 kb linearized plasmid was electrophoretically separated in 1% agarose gel and purified using Wizard SV Gel and PCR Clean-up System (Promega). The Pbxl-xyr1-t fragment was isolated after complete digestion of pUC119-Pbxl-xyr1-t with KpnI restriction enzyme and gel purification as described above. The 5.0 kb xyr1 expression cassette was ligated into linearized pNclBgl-NSN(r)* generating final transformation vector pPbxl:xyr1-pyr4 (FIG. 4A).

Example 4 Generation of Modified Host Filamentous Fungus Overexpressing Xyr1 Transcription Factor

The pPbxl-xyr1-pyr4 transformation vector was introduced into T. reesei strains P285-6aux and P491P6 and the pPS-bxl:xyr1-hph transformation vector was introduced into the RutC30 wild type strain using PEG-mediated protoplast transformation method. About 5×10⁶ spores of selected strain spores were plated onto sterile cellophane placed on PDA supplemented with 5 mM uridine and incubated for 20 hours at 30° C. Cellophane discs with mycelia were transferred to 10 mL of a protoplast preparation solution containing 7.5 g/L Driselase and 4 g/L beta-glucanase (InterSpex Products Inc., Cat. #0465-1 and 0439-2, respectively) in 50 mM potassium phosphate buffer, pH 6.5 containing 0.6 M ammonium sulfate (Buffer P). The mycelia were digested for 5 hours at 28° C. with gentle agitation at 60 rpm. Protoplasts were collected by centrifugation at 1000-1500×g for 10 min at room temperature and washed with 5 mL of Buffer P. The pellet was resuspended in 1 mL of STC buffer (1.2 M sorbitol, 10 mM CaCl₂, 10 mM Tris-HCL, pH 7.5), separated from undigested mycelia by filtration through sterile No. 60 MIRACLOTH™ and collected into a sterile microcentrifuge tube. For transformation, 0.1 mL of protoplast suspension (approximately 5×10⁶ protoplasts) was combined with 10 μg of linearized vector DNA, and 25 μL of PEG solution (25% PEG 4000, 50 mM CaCl₂, 10 mM Tris-HCl, pH 7.5). Protoplasts with DNA were incubated on ice for 30 min then 1 mL of PEG solution was added and the mixture incubated for 5 min at room temperature. Transformation mix was diluted with 2 mL of 1.2 M sorbitol in PEG solution.

Four 0.75 mL aliquots of the transformation mix with pPbxl-xyr1-pyr4 plasmid and protoplasts of strain P285-6aux or P491P6 were added into 25 mL of molten MMSS agar media (see below) cooled to about 47-50° C. and the protoplast suspensions were poured over MM agar (see below). Plates were incubated at 30° C. until colony growth was visible. Transformants were transferred to individual plates containing MM agar and allowed to sporulate. Spores were collected and plated at high dilution on MM agar to isolate homokaryon transformants, which were then plated onto PDA (Difco) and incubated at 30° C. for sporulation and subsequent genetic analysis.

Four 0.75 mL aliquots of the transformation mix with RutC30 protoplasts and pSP-bxl:xyr1-hph plasmid were added into 25 mL of PDA media cooled to about 47-50° C. and the protoplast suspensions were poured into 150 mm diameter Petri dishes. After 5 h incubation at 30° C., 25 mL of overlay media scontaining 80 U/mL of hygromycin was added. Plates were incubated at 30° C. until colony growth was visible. Transformants were transferred to individual plates containing PDA agar with 40 U/mL of hygromycin for secondary selection. Isolated stable transformants were transferred to PDA media and allowed to sporulate. Spores were collected and plated at high dilution on PDA with 40 U/mL of hygromycin to isolate homokaryon transformants, which were then plated onto PDA (Difco) and incubated at 30° C. for sporulation and subsequent genetic analysis.

Minimal medium (MM) agar: Component* Amount for 1 L of medium KH₂PO₄ 10 g (NH₄)₂SO₄ 6 g Na₃Citrate-2H₂O 3 g FeSO₄•7H₂O 5 mg MnSO₄•H₂O 1.6 mg ZnSO₄•7H₂O 1.4 mg CaCl₂•2H₂O 2 mg Agar 20 g 20% Glucose f.s. 50 ml 1 M MgSO4•7H₂O f.s. 4 mL pH to 5.5 *MMSS agar contains the same components as MM agar plus 1.2 M sorbitol, 4 mM MgSO₄, 1 g/L YNB (Yeast Nitrogen Base w/o Amino Acids from DIFCO Cat. No. 291940) and 0.12 g/L amino acids (-Ura DO Supplement from CLONTECH Cat. No. 8601-1).

Example 5 Genetic Characterization of Modified Host Filamentous Fungi Example 5.1 Confirmation of Vector Integration into T. reesei Genome

The presence or absence of Pbxl:xyr1 expression cassette in isolated modified host filamentous fungi was assessed by PCR on isolated genomic DNA samples using specific primers as described below. For genomic DNA extraction mitotically stable transformants were sporulated on Potato Dextrose Agar. Spores were collected by overlaying the PDA plates with 1 mL of Potato Dextrose broth (PDB) medium and germinated by incubation at 30° C. for 24-36 h without shaking. Mycelia were centrifuged at 10,000 rpm in a microfuge and supernatant discarded. Pellets were resuspended in 0.25 mL of RNA lysing buffer (Stratagene RNA isolation kit Cat #400800) and equal volume of glass beads was added to each cell suspension. Microcentrifuge tubes were vortexed at maximum speed for 3 min to shear the mycelia. An equal volume of phenol:chloroform:isoamyl alcohol was added and the microcentrifuge tubes vortexed for 30 sec. Finally, 0.4 mL of TE buffer, pH 7.5 was added and the microcentrifuge tubes vortexed for 30 sec. The aqueous phase was separated by microcentrifugation at 13,000 rpm for 10 min and transferred to fresh tubes. The genomic DNA was precipitated by adding 1/10 volume of 3M sodium acetate (pH 5.2) and 2.5 volumes of 100% ethanol. DNA was pelleted by centrifugation at 13,000 rpm for 10 min. Pellers were washed with 70% ethanol. dried at room temperature and then dissolved in 30-40 μL of sterile water containing RNaseA (0.005 mg/mL). One microliter of genomic DNA was used in following PCR reactions.

PCR analysis of the genomic DNA isolated from putative modified host filamentous fungi was used to confirm the integration of the Pbx:xyr1 expression cassette. The PCR was performed using primers AC124 (Pbxl forward) TTGAGCGCAGCATCACTGTGTAGA (SEQ ID NO: 17) and AC127 (xyr1 reverse), AACGGATCTGCGTCTGTGTCTGAT SEQ ID NO: 18 were used. GoTaq DNA polymerase (Promega) with an annealing temperature of 55° C. 1.5 min of extension time for 30 amplification cycles. Positive transformants were identified by amplification of a 1 kb PCR products containing Pbx:xyr1 expression cassettes from genomic DNA. No 1 kb PCR products were detected for parent strains P285-6aux (FIG. 4B), RutC30 and P491P6 (data not shown) indicating the absence of recombinant DNA Strains P692B, P692A, RutC30-R3, P1194E, P1194F, P1197B were identified as positive modified host filamentous fungi and selected for further analysis.

Example 5.2 Expression Levels of Xyr1 and (Hemi)Cellulase Genes

To determine transcription levels of xyr1 and selected (hemi)cellulase genes, the total RNA was isolated from mycelia of modified host filamentous fungi and parental strains grown in the Liquid Growth medium.

Liquid growth medium: Component Final concentration Glucose 10 g/L Xylose 10 g/L Cellobiose 2.5 g/L Ammonium Sulphate 6 g/L 3xNa-Citratedihydrate 3 g/L KH₂PO₄ 10 g/L MgSO₄•7H₂O 4 mM CaCl₂•2H₂O 2 mg/L ZnSO4•7H₂O 1.4 mg/L FeSO₄•7H₂O 5 mg/L MnSO₄•7H₂O 1.6 mg/L

Culture tubes containing 5 mL of the Liquid Growth medium were inoculated with spores of modified host filamentous fungi and shaken at 30° C. for 4 days. The biomass was filtered through GF/A microfiber paper, washed with sterile water and frozen in liquid nitrogen. The isolation of RNA and qRT-PCR reactions were performed as described in Example 2.2. The primer pairs used for assessment of transcription levels of xyr1, cel7a, cel7b, xyn1, xyn2 and bxl1 genes are listed in Table 6.

TABLE 6 Primers used for qRT-PCR analysis of modified host filamentous fungi overexpressing Xyr1 transcription factor and parental filamentous fungi. SEQ ID NO Primer name Primer sequence 1 Ntf2F ACAGAGTTGGCATTGTAGACAGCG 2 Ntf2R CGAGTAAAGCACACAAACCGCCAA 3 Xyr1F AGCCAGATTCTCGAGTTTGACCCT 4 Xyr1R GCAAGCTTCGTGTGCCCTAACAAT 7 Ce17aQ1F TACTCTGGCAACGAAGCTCAACGAT 8 Ce17aQ1R GCCACAGCATGTTGGCGTAGTAA 11 Ce17bF ATCACCCGCAAGTACCAGCAAA 12 Ce17bR CTGGCTGTTGTCGTTCCAAATGCT 15 Xyn1F TCATCAACTTCTCGGGCAGCTACA 16 Xyn1R AGGTGCCAAAGTTCTCGACGATGT 19 Xyn2F ACGGCTACTTCTACTCGTACTGGA 20 Xyn2R TGTAGCTGCCCGAGAAGTTGATGA 21 Bxl1F TATACGGCCATGCTGTTTGTTCGC 22 Bxl1R TGGAAGAGTGACCAGGCTTGATGT

All modified host filamentous fungi tested containing Pbxl:xyr1 expression cassette showed at least 2-fold increase in xyr1 transcript levels when grown on a carbon source comprising glucose, HDC (xylose) and CIC (cellobiose) relative to xyr1 transcript levels in the corresponding parental filamentous fungi grown with the same carbon source. For example, the modified host filamentous fungi, strains P692B and RutC30-R3, produced at least 2-fold higher levels of xyr1 transcript when grown on 100% xylose and 100% arabinose as compared to its parental filamentous fungi, strains P285-6 and RutC30 (FIGS. 5A and B). This resulted in significant increase in cel7a, cel7b and xyn1 transcript levels in the Xyr1 overexpression strains relative to those in the corresponding parental strain when the fermentation carbon source was 100% HDC (xylose or arabinose). The lowest effect of xyr1 overexpression was observed on the transcript levels of bxl1 and xyn1.

Example 6 Effect of Xyr1 Overexpression on Cellulase Production by Modified Host Filamentous Fungi

Different types of carbon sources (e.g. glucose+CIC, 100% xylose, 100% arabinose and a blend of 50 wt % glycerol, 25 wt % glucose and 25 wt % xylitol) were used in 14 L fermentations. All fermentations and the assessment of the q_(p), biomass and protein production were performed as described in Example 2.1. Highly productive T. reesei strains on glucose+CIC usually produce 30-45 g/L of total protein during 160-180 hrs in 14 L pilot scale fermentation. The maximum q_(p) is reached at about 40-60 hrs of fermentation time and declines at the end of fermentation. Parental strains, P285-6, P491P and RutC30, showed usual fermentation performance indicators on glucose+CIC (Table 2) suggesting that the introduction of the additional copy of xyr1 gene under control of bxl1 promoter did not significantly affect cellulase gene expression under these. However, since the extra copy of xyr1 in P692B is expressed under the control of the bxl1 promoter, and the bxl1 gene is poorly expressed during fermentation on glucose+CIC as a feed, it is possible that the expression levels of xyr1 transcription factor did not increase significantly and, thus, it was not sufficient to increase cellulase production.

The maximum q_(p) and the amount of total protein (in g/L) produced by the modified host filamentous fungi, strains P692B, P692A, RutC30-R3, P1197 B, P1194E and P1194F, during the fermentations on 100% xylose increased about 4- and 3-fold compared to those of the corresponding parental filamentous fungi, strains P285-6, RutC30 and P491P, respectively (Table 2). Moreover, the modified host filamentous fungi accumulated significantly less biomass in fermentations with 100% xylose as carbon source than their corresponding parental filamentous fungi (Table 2).

Similar benefits of increased q_(p) and protein yield were observed when the modified host filamentous fungi, strains P692A and RutC30-R3, were grown on other HDC (100% arabinose or a blend with 50 wt % glycerol/25 wt % glucose and 25 wt % xylitol) as carbon source over their respective parental filamentous fungus, strains P285-6 and RutC30 (Table 2). In some instances, as when arabinose was used as the carbon soured, the fermentation process with modified host filamentous fungus (strain P692A) produced more, not less, biomass than the process with the corresponding parental filamentous fungus (strain P285-6) in addition to achieving higher protein yields (FIG. 10). This manifests in a higher average q_(p), indicating that the overexpression of xyr1 activates not only cellulase gene expression in arabinose-fed cultures, but also an overall more effective metabolism of arabinose.

Example 7 Analysis of Cellulase and Hemicellulase Components in Cellulase Mixtures Produced by Modified Host Filamentous Fungi Overexpressing Xyr1 Example 7.1 Determining the Relative Proportions of Cellulase and Hemicellulase Components Cellulase Mixtures Produced in 14 L Fed-Batch Fermentations

The relative concentrations (in wt % of total secreted protein) of four cellulase components (Cel7A, Cel6A, Cel7B, Cel5A) and the two xylanase components, (Xyn1 and Xyn2) were determined by ELISA. Culture filtrates from 14 L fermentations and purified component standards were diluted to 0.01-10 μg/mL in phosphate-buffered saline, pH 7.2 (PBS) and incubated overnight at 4° C. in microtitre plates (Costar EIA #9018). These plates were washed with PBS containing 0.1% Tween-20 (PBS/Tween) and then incubated in PBS containing 1% bovine serum albumin (PBS/BSA) for 1 hr at room temperature. Blocked microtitre wells were washed with PBS/Tween. Rabbit polyclonal antisera specific for Cel7A, Cel6A, Cel7B, Cel5A, Xyn1 and Xyn2 were diluted in PBS/BSA, added to separate microtitre plates and incubated for 2 hr at room temperature. Plates were washed and incubated with a goat anti-rabbit antibody coupled to horseradish peroxidase (Sigma #A6154), diluted 1/2000 in PBS/BSA, for 1 hr at room temperature. After washing, tetramethylbenzidine was added to each plate and incubated for 30 min at room temperature. The absorbance at 360 nm was measured in each well and converted into protein concentration using the Cel7A, Cel6A, Cel7B, Cel5A, Xyn1 and Xyn2 standard curves. The concentration of each component was expressed as the mass percent of the component as a fraction of total secreted protein. In one manner of analyzing these results, the concentrations of Cel7A, Cel6A, Cel7B and Cel5A were summed in each respective enzyme and collectively referred to as Cellulase in Table 3. Similarly, the concentrations of Xyn1 and Xyn2 were summed in each respective enzyme and collectively referred to as Xylanase in Table 3. The use of these terms does not imply that there are not other secreted proteins, which were not tested for here by ELISA, that could also be considered cellulase or xylanase.

The ELISA results are presented in FIGS. 9B, 10B and 11B. These results show the relative proportion (in wt % of total secreted protein) of Cel7A, Cel6A, Cel7B, Cel5A, Xyn1 and Xyn2 in the cellulase mixture produced in fermentation processes using modified host or parental filamentous fungi with carbon source comprising HDC or CIC. The relative proportion of representative cellulase (Cel7A+Cel6A+Cel7B+Cel5A) and representative xylanase (Xyn1+Xyn2) in wt % of total secreted protein are shown in Table 3.

The relative proportion of cellulase components produced by the parental filamentous fungi, strains P285-6 and RutC30, during in a fermentation process where the carbon source comprised only HDC were 3- to 5-fold lower when compared to that produced in a fermentation process where the carbon source comprised glucose+CIC (FIGS. 9B and 10B and Table 3). In particular, the proportion of xylanase (Xyn1+Xyn2) increased from about 2 wt % of total secreted protein on glucose+CIC up to about 35 wt % on HDC (FIGS. 9B, 10B and Table 3).

The overexpression of xyr1 in the modified host filamentous fungi (strains P692B and RutC30-R3) resulted in 1.5- to 3-fold increase in the production of cellulase components (Cel7A, Cel6A, and Cel7B) in fermentations with 100% xylose or arabinose over the production of cellulase components by the corresponding parental filamentous fungis (strain P285-6 and RutC30) on the same carbon sources (FIGS. 9B and 10B and Table 3). Furthermore, the relative proportion of cellulase components in the cellulase mixture produced by modified host filamentous fungi that overexpress xyr1 (trains P692B and RutC30-R3) decreased less markedly, and the proportion of xylanase increased less markedly when the carbon source supplied to the fermentation process was 100% arabinose or xylose as compared to the cellulase mixture produced by the same strains in a fermentation process using glucose+CIC as the carbon source (FIGS. 9B and 10B and Table 3).

Fermentations on pure sugar and glycerol mix as a carbon source revealed that the production of hemicellulase significantly decreased when 50% glucose/25% glycerol/25% xylitol was used as a carbon source compared to that produced on 50% glucose/25% glycerol/25% xylose as a carbon source (Table 3, FIG. 9B).

Example 7.2 Beta-Xylosidase Content in Cellulase Mixtures Produced by Modified Host and Parental Filamentous Fungi

The relative concentration of beta-xylosidase was calculated using Agilent Bioanalyzer 2100 using Protein Kit 230 as described in manufactures protocol. The beta-xylosidase, in wt % of total protein, produced in each fermentation is indicated in Table 3. As expected all parental filamentous fungi (strains P285-6, RutC30 and P491P) produced cellulase mixtures with a high relative proportion of beta-xylosidase in fermentation processes using HDC as a carbon source. Modified host filamentous fungi overexpressing xyr1 (strain P692B, RutC30-R3, P1194E, P1194F and P1197B) produced cellulase mixtures with up to 15-fold lower relative proportions of beta-xylosidase proportions in fermentation processed using the same HDC as carbon sources (Table 3). However, the relative proportion of Cel74A (xyloglucanase) in these cellulase mixtures (produced by the modified host filamentous fungi) increased up to 12 wt % of total protein while this protein was not detected in cellulase mixtures produced by the corresponding parental filamentous fungi grown on all types of carbon sources tested (data not shown).

Modified host filamentous fungi (strains P692B and RutC30-R3), when grown in fermentation processes in which the carbon source was 50 wt % glycerol/25 wt % glucose/25 wt % xylitol, produced cellulase mixtures with further reduced relative proportions of beta-xylosidase compared to fermentation processes in which the carbon source was 100% xylose or 50 wt % glycerol/25 wt % glucose/25 wt % xylose (Table 3).

Example 8 The Cellulose Hydrolysis Activity of Cellulase Mixtures Produced by Parental and Modified Host Filamentous Fungi

The cellulose hydrolysis activity of cellulase mixtures produced by modified host filamentous funi overexpressing xyr1 and corresponding parental filamentous in fermentation processes using different carbon sources was assessed as described in U.S. patent application Ser. No. 11/846,653. The cellulase mixture produced from each fermentation process was tested in a 0.25 mL mixed cellulose hydrolysis assay. The cellulase mixtures were diluted in citrate buffer containing 0.5% sodium benzoate, complemented with a beta-glucosidase preparation from Aspergillus niger and incubated with acid pretreated wheat straw. The pretreatment was carried out as per Foody, U.S. Pat. No. 4,461,648. Incubation was at 50° C. for 24 hr and the target cellulose conversion level was greater than 70%. The activity of the cellulase mixtures was calculated by determining the amount of enzyme required to reach the target cellulose conversion level. The activity associated with cellulase mixtures produced by fermentations of parental modified host filamentous fungi (strains P285-6, P692A and P692B) were normalized to the cellulose hydrolysis activity of cellulase mixtures produced by the parental filamentous fungi (strain P285-6) using glucose+CIC as carbon source (fermentation number 2404). Similarly, the activity associated with cellulase mixtures produced by fermentations of parental and modified host filamentous fungi (strains RutC30, RutC30-R3, M2C38, P491P, P1194E, P1194F and P1197B) were normalized to the cellulose hydrolysis activity of cellulase mixtures produced by the parental filamentous fungi (strain RutC30) using glucose+CIC as carbon source (ferrmentation number 4279). These results are referred to as ‘Relative Activity’ in FIGS. 9A, 11A and 12 A and in Table 3.

A small increase in activity of the cellulase mixture produced by P692B (fermentation numbers 3796 and 3963) was observed, relative to the activity of the P285-6 cellulase mixture, when glucose+CIC was used as the carbon source for fermentation (FIG. 9 a and Table 3). This likely reflects a slight improvement in cellulase composition in respect of total secreted protein as discussed in Example 7.1.

As a result of the significantly increased proportion of cellulase components in the cellulase mixture protein produced by strain P692B in fermentation processes using 100% xylose or arabinose, the cellulose hydrolysis activity increased by 4- and 2-fold respectively compared to that of cellulase mixture produced by the parental strain P285-6 in a similar fermentation process (FIG. 9A and Table 3).

Similarly, the improved cellulase composition produced by strain P692B in a fermentation process in which the carbon source comprised xylitol rather than xylose correlates with up to 2-fold increase in cellulose hydrolyzing activity of the cellulase mixture produced by this modified host filamentous fungus as compared to that of the cellulase mixture produced by the parental filamentous fungus (strain P285-6) in similar fermentation processes. (Table 3 and FIG. 9A).

The deletion of xylanase 2 in P491P strain did not change the relative proportion of cellulase components in the cellulase mixtures compared to that in the cellulase mixtures produced by the its parent strain M2-C38. This is likely due to the low fermentation pH at which mainly xylanase 1 is expressed. However, as observed with P692B and RutC30-C3 modified host filamentous fungi, the overexpression of Xyr1 possibly results in loss of pH dependent expression and both xylanases are produced in similar abundance. Further, the deletion of xyn2 in the presence of Xyr1 overexpression resulted in about 3-fold increase in the proportion of cellulase components in the cellulase mixture and thus, improved cellulase activity (Table 3).

Further, the absence of significant difference in the proportion of cellulase components in the cellulase mixtures produced by strains M2-C38 and P491P strains was reflected in similar cellulase hydrolytic activity. The overexpression of Xyr1 in the presence of xyn2 deletion increased cellulase activity by about 2-fold in the cellulase mixtures produced by the modified host filamentous fungal strains P1194E, P1194F and P1197B transformants compared to that of the cellulase mixtures produced by parental strains M2-C38 and P491P.

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1. A fermentation process for the production of a cellulase mixture, said process comprising: a) providing a modified host filamentous fungus that overexpresses a Xyr1 transcription factor or a Xyr1 equivalent transcription factor; and b) culturing the modified host filamentous fungus of step a) in a medium comprising a carbon source, wherein the carbon source contains from about 60 wt % to about 100 wt % of a hemicellulose-derived carbohydrate and from about 0 wt % to about 3 wt % of a cellulase-inducing carbohydrate to produce a cellulase mixture; wherein the cellulase mixture has an increase in cellulase activity of at least about 1.7-fold relative to that of a cellulase mixture produced by a parental filamentous fungus that does not overexpress the Xyr1 transcription factor or the Xyr1 equivalent transcription factor when cultured in the same medium.
 2. The fermentation process of claim 1, wherein the Xyr1 protein is selected from the group consisting of: a) a protein comprising the amino acid sequence of SEQ ID NO:27; b) a protein with an amino acid sequence exhibiting from about 90% to about 100% identity to the amino acid sequence of SEQ ID NO:27; and c) a protein containing zinc binuclear cluster that possesses similar DNA binding activity specific to a GGC(T/A)₃-like consensus motif in cellulase and/or hemicellulase promoters as that of the protein comprising the amino acid sequence of SEQ ID NO:27.
 3. The fermentation process of claim 1, wherein the Xyr1 equivalent transcription factor is selected from the group consisting of: a) a protein with an amino acid sequence exhibiting from about 45% to about 99% identity to the amino acid sequence of SEQ ID NO: 27, b) a protein with an amino acid sequence exhibiting from about 90% to about 99% identity to the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35, or c) a protein containing a zinc binuclear cluster that that possesses equivalent DNA binding activity specific to a consensus sequence GGC(T/A)₃-like motif within cellulase and/or hemicellulase promoter sequences as the protein with the amino acid sequence of SEQ ID NO:
 27. 4. The fermentation process of claim 1, wherein the modified host filamentous fungus is partially or completely deficient in expressing one or more hemicellulase enzyme.
 5. The fermentation process of claim 4, wherein the one or more hemicellulase enzyme is selected from the group consisting of a xylanase, a beta-xylosidase, an alpha-arabinofuranosidase, a beta-mannanase, an alpha-glucuronidase, a acetyl xylan esterase and a combination thereof.
 6. The fermentation process of claim 5, wherein the one or more hemicellulase enzyme is selected from the group consisting of a xylanase, a beta-xylosidase and a combination thereof.
 7. A fermentation process for the production of a cellulase mixture comprising: a) genetically modifying a host filamentous fungus to overexpress a Xyr1 transcription factor or a Xyr1 equivalent transcription factor; and b) culturing the host filamentous fungus of step a) in a medium comprising a carbon source, wherein the carbon source contains from about 60 wt % to about 100 wt % of a hemicellulose-derived carbohydrate, and no cellulase-inducing carbohydrate, or less than about 5 wt % of a cellulase-inducing carbohydrate to produce a cellulase mixture; wherein the cellulase mixture has an increase in cellulase activity of at least about 1.7-fold relative to that of a cellulase mixture produced by a parental filamentous fungus that does not overexpress the Xyr 1 transcription factor or the Xyr1 equivalent transcription factor when cultured in the same medium.
 8. The fermentation process of claim 7, wherein the step of genetically modifying comprises a) transforming the host filamentous fungus with a Xyr1 genetic construct in which a nucleic acid sequence encoding a Xyr1 transcription factor or a Xyr1 equivalent transcription factor is operatively linked to a promoter nucleic acid sequence; and b) selecting those transformants from step a) containing the Xyr1 genetic construct.
 9. The fermentation process of claim 7, wherein the Xyr1 protein is selected from the group consisting of: a) a protein comprising the amino acid sequence of SEQ ID NO:27; b) a protein with an amino acid sequence exhibiting from about 90% to about 100% identity to the amino acid sequence of SEQ ID NO:27; and c) a protein containing zinc binuclear cluster that possesses similar DNA binding activity specific to a GGC(T/A)₃-like consensus motif in cellulase and/or hemicellulase promoters as that of the protein comprising the amino acid sequence of SEQ ID NO:27.
 10. The fermentation process of claim 7, wherein the Xyr1 equivalent transcription factor is selected from the group consisting of: d) a protein with an amino acid sequence exhibiting from about 45% to about 99% identity to the amino acid sequence of SEQ ID NO: 27, e) a protein with an amino acid sequence exhibiting from about 90% to about 99% identity to the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35, or f) a protein containing a zinc binuclear cluster that that possesses equivalent DNA binding activity specific to a consensus sequence GGC(T/A)₃-like motif within cellulase and/or hemicellulase promoter sequences as the protein with the amino acid sequence of SEQ ID NO:
 27. 11. The fermentation process of claim 8, wherein the promoter nucleic acid sequence is native or heterologous to the host filamentous fungus.
 12. The fermentation process of claim 8, wherein the promoter nucleic acid sequence is derived from a gene whose expression is induced during growth of the host filamentous fungus on a carbon source comprising hemicellulose derived carbohydrates.
 13. The fermentation process of claim 12, wherein the promoter nucleic acid sequence is derived from a gene selected from the group consisting of T. reesei bxl1, T. reesei xln1 and T. reesei xln2.
 14. The fermentation process of claim 8, wherein the promoter nucleic acid sequence is from a gene whose expression is constitutive during growth of the host filamentous fungus.
 15. The fermentation process of claim 7, wherein the step of genetically modifying further comprises modifying one or more gene in said host filamentous fungus encoding a hemicellulase enzyme selected from the group consisting of xylanases, beta-xylosidases, alpha-arabinofuranosidases, beta-mannanases, alpha-glucuronidases, acetylxylan esterase and a combination thereof, so that said host filamentous fungus is partially or completely deficient in expressing the one or more hemicellulase enzyme.
 16. The fermentation process of claim 15, wherein said one or more hemicellulase enzyme is selected from the group consisting of a xylanase and a beta-xylosidase.
 17. The fermentation process of claim 1, wherein the process produces a cellulase mixture comprising from about 40 wt % to about 100 wt % cellulase components.
 18. The fermentation process of claim 7, wherein the process produces a cellulase mixture comprising from about 40 wt % to about 100 wt % cellulase components.
 19. The fermentation process of claim 1, wherein the process is characterized by having at least about a 2-fold increase in specific productivity (q_(p)) relative to an equivalent process utilizing a parental filamentous fungus does not overexpress Xyr1.
 20. The fermentation process of claim 7, wherein the process is characterized by having at least about a 2-fold increase in specific productivity (q_(p)) relative to an equivalent process utilizing a parental filamentous fungus does not overexpress Xyr1.
 21. The fermentation process of claim 1, wherein the host filamentous fungus is a species of Trichoderma, Hypocrea, Aspergillus, Humicola, Fusarium, Penicillium, Neurospora, Phanerochaete, Agaricus, Chaetomium, or Magnaporthe.
 22. The fermentation process of claim 21, wherein the host filamentous fungus is Trichoderma reesei or Hypocrea jecorina.
 23. The fermentation process of claim 7, wherein the host filamentous fungus is a species of Trichoderma, Hypocrea, Aspergillus, Humicola, Fusarium, Penicillium, Neurospora, Phanerochaete, Agaricus, Chaetomium, or Magnaporthe.
 24. The fermentation process of claim 23, wherein the host filamentous fungus is Trichoderma reesei or Hypocrea jecorina.
 25. The fermentation process of claim 1, wherein the medium comprises one or more additional carbon sources.
 26. The fermentation process of claim 25, wherein the one or more additional carbon source is glycerol, one or more sugar alcohols or an organic acid.
 27. The fermentation process of claim 26, wherein the one or more sugar alcohols is xylitol.
 28. The fermentation process of claim 7, wherein the medium comprises one or more additional carbon sources.
 29. The fermentation process of claim 28, wherein the one or more additional carbon source is glycerol, one or more sugar alcohols or an organic acid.
 30. The fermentation process of claim 29, wherein the one or more sugar alcohols is xylitol.
 31. The fermentation process of claim 1, wherein the step of culturing is conducted at a temperature of from about 20° C. to about 35° C. and a pH of from about 3.0 to about 6.5.
 32. The fermentation process of claim 7, wherein the step of culturing is conducted at a temperature of from about 20° C. to about 35° C. and a pH of from about 3.0 to about 6.5.
 33. The fermentation process of claim 1, wherein the process is fed-batch.
 34. The fermentation process of claim 7, wherein the process is fed-batch.
 35. The fermentation process of claim 1, wherein the process is continuous.
 36. The fermentation process of claim 7, wherein the process is continuous.
 37. The fermentation process of claim 1, wherein the process is conducted aerobically.
 38. The fermentation process of claim 7, wherein the process is conducted aerobically.
 39. The fermentation process of claim 1, wherein the cellulase-inducing carbohydrate is selected from the group consisting of cellulose, lactose, cellobiose, sophorose, gentiobiose and a combination thereof.
 40. The fermentation process of claim 7, wherein the cellulase-inducing carbohydrate is selected from the group consisting of cellulose, lactose, cellobiose, sophorose, gentiobiose and a combination thereof.
 41. The fermentation process of claim 1, wherein the carbon source contains comprises 0 wt % cellulase-inducing carbohydrate.
 42. The fermentation process of claim 7, wherein the carbon source contains comprises 0 wt % cellulase-inducing carbohydrate.
 43. A process for the hydrolyzing a cellulose substrate comprising contacting said substrate with a cellulase mixture produced by the fermentation process of claim
 1. 44. The process of claim 43, wherein the cellulose substrate is a pretreated lignocellulosic feedstock.
 45. A process for the hydrolyzing a cellulose substrate comprising contacting said substrate with a cellulase mixture produced by the fermentation process of claim
 7. 46. The process of claim 45, wherein the cellulose substrate is a pretreated lignocellulosic feedstock.
 47. A fermentation process for the production of a cellulase mixture, said process comprising: a. providing a modified host filamentous fungus that overexpresses a Xyr1 or a Xyr1 equivalent transcription factor; and b. culturing the modified host filamentous fungus of step a) in a medium comprising a carbon source, wherein the carbon source contains from about 25 wt % to about 100 wt % of a hemicellulose-derived sugar alcohol, about 0 wt % of a cellulase-inducing carbohydrate and from about 0 wt % to about 75 wt % glucose, glycerol or a combination thereof, to produce a cellulase mixture; wherein the cellulase mixture has an increase in cellulase activity of at least about 1.7-fold relative to that of a cellulase mixture produced by a parental filamentous fungus that does not the overexpress Xyr 1 transcription factor or the Xyr1 equivalent transcription factor when cultured in the same medium.
 48. The fermentation process of claim 47, wherein the hemicellulose-derived sugar alcohol is xylitol.
 49. The fermentation process of claim 48, wherein the carbon source contains from about 0 wt % to about 25 wt % glycerol and from about 0 wt % to about 50 wt % glucose. 